Importing libraries

In [ ]:
import numpy as np
import pandas as pd
%matplotlib inline
import matplotlib.pyplot as plt
import seaborn as sns
from sklearn.decomposition import PCA
from scipy import stats
from sklearn.mixture import GaussianMixture

from sklearn.model_selection import train_test_split
from sklearn import feature_selection
from sklearn import model_selection
from sklearn.metrics import accuracy_score 
from sklearn.linear_model import LogisticRegression
from sklearn.svm import SVC
from sklearn.naive_bayes import GaussianNB
from sklearn.ensemble import RandomForestClassifier,GradientBoostingClassifier
from sklearn.neighbors import KNeighborsClassifier
from scipy.sparse import csr_matrix
from numpy import count_nonzero
from scipy.sparse import lil_matrix
from scipy import sparse
from scipy.stats import uniform
import pandas as pd
import sys
import numpy as np
from numpy import mean
from numpy import std
from numpy.random import randn
from numpy.random import seed
from matplotlib import pyplot
from sklearn.mixture import GaussianMixture
from scipy import stats

import warnings
warnings.filterwarnings('ignore')

Reading files

To use if running with colab, otherwise, ignore.\ Please, put the files in the same folder in the same folder the notebook is.

In [ ]:
from google.colab import drive
drive.mount('/content/drive')
%cd '/content/drive/My Drive/'
Drive already mounted at /content/drive; to attempt to forcibly remount, call drive.mount("/content/drive", force_remount=True).
/content/drive/My Drive
In [ ]:
MCF7_meta = pd.read_csv('MCF7_SmartS_MetaData.tsv',delimiter = '\t',  index_col = 0)
In [ ]:
HCC1806_meta = pd.read_csv('HCC1806_SmartS_MetaData.tsv',delimiter = '\t',  index_col = 0)
In [ ]:
MCF7_unf = pd.read_csv('MCF7_SmartS_Unfiltered_Data.txt', delimiter='\ ',engine='python',  index_col=0)
In [ ]:
HCC1806_unf = pd.read_csv("HCC1806_SmartS_Unfiltered_Data.txt",delimiter="\ ",engine='python',index_col=0)
In [ ]:
MCF7_f_n = pd.read_csv('MCF7_SmartS_Filtered_Normalised_3000_Data_train.txt', delimiter = '\ ', index_col=0,engine='python')
In [ ]:
HCC1806_f_n= pd.read_csv('HCC1806_SmartS_Filtered_Normalised_3000_Data_train.txt', delimiter = '\ ', index_col=0,engine='python')
In [ ]:
MCF7_drop_f_n = pd.read_csv('MCF7_Filtered_Normalised_3000_Data_train.txt', delimiter = '\ ', index_col=0,engine='python')
In [ ]:
HCC1806_drop_f_n = pd.read_csv('HCC1806_Filtered_Normalised_3000_Data_train.txt', delimiter = '\ ', index_col=0,engine='python')

DATA ANALYSIS

Introduction

The overall aim of the AI Lab is to build a classification device able to predict, by exploiting which genes are expressed in a particular cell and in what quantity, whether the cell is under normoxia condition or hypoxic condition.\ An hypoxic cell is a cell that doesn't receive much $O_2$. There are different stages of hypoxia, and the data used in this project have been obtained by sequencing cancer cells that had previously been subjected to two different possible conditions: normal oxygen level equal to (~21% of $O_2$) and hypoxic oxigen level (~1% of $O_2$).\ Being able to predict if a cell is in hypoxic condition could be of fundamental importance as cells under this condition have greater resistance to cancer treatments.

Materials and Methods

The datasets come from two different cell lines, HCC1806 and MCF7 respectively, both made up of cells from women with breast cancer.\ These data were obtained by sequencing (using Smart-Seq and Drop-Seq) the samples. After the sequencing process, we have some data showing whether a specific gene is present and in what quantity is expressed in that specific cell.

First, we will do an exploratory data analysis using both the complete (unfiltered) datasets and those already filtered and normalized.\ In this phase we tried to understand the size of the dataset and if there were particular behaviors to be studied in details later. Additionally, one of the main objectives of this first phase was to try to understand, since the dataset was very sparse, how the size of the dataset could be reduced without losing information.\ In the central part of our work, we exploited PCA and clustering to gain a deeper understanding and begin to identify which patterns could be crucial in identifying the condition of hypoxia.\ Finally, using the Support Vector Machine, logistic regression, random forests classifiers and neural networks, we developed a tool capable of classifying the condition under which a cell had been subjected.

SMART SEQ EXPERIMENT

Meta data

Firstly we download the meta_data files that provide important information on how the experiments were conducted on the single cell.\ It is organized as follows: each row represents the sequencing of RNA done on a single cell using pcr technique. Each column specifies how the experiment was performed: 'cell line', 'plate', 'position of the cell', 'condition in which the cell was exposed and other information related to experiment'. The file's rows correspond to the column's name of the file we want to analyze.

In [ ]:
# Print the dimensions of the file
print("Dataframe dimensions:", np.shape(MCF7_meta))
# >Display the first 5 rows
MCF7_meta.head()
Dataframe dimensions: (383, 8)
Out[ ]:
Cell Line Lane Pos Condition Hours Cell name PreprocessingTag ProcessingComments
Filename
output.STAR.1_A10_Hypo_S28_Aligned.sortedByCoord.out.bam MCF7 output.STAR.1 A10 Hypo 72 S28 Aligned.sortedByCoord.out.bam STAR,FeatureCounts
output.STAR.1_A11_Hypo_S29_Aligned.sortedByCoord.out.bam MCF7 output.STAR.1 A11 Hypo 72 S29 Aligned.sortedByCoord.out.bam STAR,FeatureCounts
output.STAR.1_A12_Hypo_S30_Aligned.sortedByCoord.out.bam MCF7 output.STAR.1 A12 Hypo 72 S30 Aligned.sortedByCoord.out.bam STAR,FeatureCounts
output.STAR.1_A1_Norm_S1_Aligned.sortedByCoord.out.bam MCF7 output.STAR.1 A1 Norm 72 S1 Aligned.sortedByCoord.out.bam STAR,FeatureCounts
output.STAR.1_A2_Norm_S2_Aligned.sortedByCoord.out.bam MCF7 output.STAR.1 A2 Norm 72 S2 Aligned.sortedByCoord.out.bam STAR,FeatureCounts

The MCF7 metadata dataframe has 383 rows.

This means that, in the MCF7 unfiltered dataframe, we'll have 383 cells (columns).

In [ ]:
# Display the bottom 5 rows
MCF7_meta.tail(5)
Out[ ]:
Cell Line Lane Pos Condition Hours Cell name PreprocessingTag ProcessingComments
Filename
output.STAR.4_H5_Norm_S359_Aligned.sortedByCoord.out.bam MCF7 output.STAR.4 H5 Norm 72 S359 Aligned.sortedByCoord.out.bam STAR,FeatureCounts
output.STAR.4_H6_Norm_S360_Aligned.sortedByCoord.out.bam MCF7 output.STAR.4 H6 Norm 72 S360 Aligned.sortedByCoord.out.bam STAR,FeatureCounts
output.STAR.4_H7_Hypo_S379_Aligned.sortedByCoord.out.bam MCF7 output.STAR.4 H7 Hypo 72 S379 Aligned.sortedByCoord.out.bam STAR,FeatureCounts
output.STAR.4_H8_Hypo_S380_Aligned.sortedByCoord.out.bam MCF7 output.STAR.4 H8 Hypo 72 S380 Aligned.sortedByCoord.out.bam STAR,FeatureCounts
output.STAR.4_H9_Hypo_S381_Aligned.sortedByCoord.out.bam MCF7 output.STAR.4 H9 Hypo 72 S381 Aligned.sortedByCoord.out.bam STAR,FeatureCounts
In [ ]:
# To print the dimensions of the file
print("Dataframe dimensions:", np.shape(HCC1806_meta))
# To disply the first 5 rows
HCC1806_meta.head()
Dataframe dimensions: (243, 8)
Out[ ]:
Cell Line PCR Plate Pos Condition Hours Cell name PreprocessingTag ProcessingComments
Filename
output.STAR.PCRPlate1A10_Normoxia_S123_Aligned.sortedByCoord.out.bam HCC1806 1 A10 Normo 24 S123 Aligned.sortedByCoord.out.bam STAR,FeatureCounts
output.STAR.PCRPlate1A12_Normoxia_S26_Aligned.sortedByCoord.out.bam HCC1806 1 A12 Normo 24 S26 Aligned.sortedByCoord.out.bam STAR,FeatureCounts
output.STAR.PCRPlate1A1_Hypoxia_S97_Aligned.sortedByCoord.out.bam HCC1806 1 A1 Hypo 24 S97 Aligned.sortedByCoord.out.bam STAR,FeatureCounts
output.STAR.PCRPlate1A2_Hypoxia_S104_Aligned.sortedByCoord.out.bam HCC1806 1 A2 Hypo 24 S104 Aligned.sortedByCoord.out.bam STAR,FeatureCounts
output.STAR.PCRPlate1A3_Hypoxia_S4_Aligned.sortedByCoord.out.bam HCC1806 1 A3 Hypo 24 S4 Aligned.sortedByCoord.out.bam STAR,FeatureCounts

The HCC1806 metadata dataframe has 243 rows.

This means that, in the HCC1806 unfiltered dataframe, we'll have 243 cells (columns).

In [ ]:
# To display the bottom 5 rows
HCC1806_meta.tail(5)
Out[ ]:
Cell Line PCR Plate Pos Condition Hours Cell name PreprocessingTag ProcessingComments
Filename
output.STAR.PCRPlate4H10_Normoxia_S210_Aligned.sortedByCoord.out.bam HCC1806 4 H10 Normo 24 S210 Aligned.sortedByCoord.out.bam STAR,FeatureCounts
output.STAR.PCRPlate4H11_Normoxia_S214_Aligned.sortedByCoord.out.bam HCC1806 4 H11 Normo 24 S214 Aligned.sortedByCoord.out.bam STAR,FeatureCounts
output.STAR.PCRPlate4H2_Hypoxia_S199_Aligned.sortedByCoord.out.bam HCC1806 4 H2 Hypo 24 S199 Aligned.sortedByCoord.out.bam STAR,FeatureCounts
output.STAR.PCRPlate4H7_Normoxia_S205_Aligned.sortedByCoord.out.bam HCC1806 4 H7 Normo 24 S205 Aligned.sortedByCoord.out.bam STAR,FeatureCounts
output.STAR.PCRPlate4H9_Normoxia_S236_Aligned.sortedByCoord.out.bam HCC1806 4 H9 Normo 24 S236 Aligned.sortedByCoord.out.bam STAR,FeatureCounts
In [ ]:
# Checking the data type
MCF7_meta.dtypes
Out[ ]:
Cell Line             object
Lane                  object
Pos                   object
Condition             object
Hours                  int64
Cell name             object
PreprocessingTag      object
ProcessingComments    object
dtype: object
In [ ]:
# Checking the data type
HCC1806_meta.dtypes
Out[ ]:
Cell Line             object
PCR Plate              int64
Pos                   object
Condition             object
Hours                  int64
Cell name             object
PreprocessingTag      object
ProcessingComments    object
dtype: object

We can distinguish between object type and integer type, the two cell lines have most of the characteristics in common except for 'Lane' in MCF7 and 'PCR Plate' in HCC1806

In [ ]:
list(MCF7_meta.columns)
Out[ ]:
['Cell Line',
 'Lane',
 'Pos',
 'Condition',
 'Hours',
 'Cell name',
 'PreprocessingTag',
 'ProcessingComments']
In [ ]:
list(HCC1806_meta.columns)
Out[ ]:
['Cell Line',
 'PCR Plate',
 'Pos',
 'Condition',
 'Hours',
 'Cell name',
 'PreprocessingTag',
 'ProcessingComments']
In [ ]:
# Finding the null values.
print(MCF7_meta.isnull().sum())
Cell Line             0
Lane                  0
Pos                   0
Condition             0
Hours                 0
Cell name             0
PreprocessingTag      0
ProcessingComments    0
dtype: int64

The output tells us that no row has all 0 values

The meta_data files are organized as follows: the rows are the sequencing of rna done on a single cell using pcr technique (x383 for MCF7, x243 for HCC1806). The columns specify how the experiment was performed, 'cell line', 'plate', position of the cell, condition[...]

Unfiltered data

MCF7

We start by analyzing the MCF7 unfiltered dataset.

Understanding the data
In [ ]:
# To display the first 5 rows of the unfiltered MCF7 data
MCF7_unf.head()
Out[ ]:
"output.STAR.1_A10_Hypo_S28_Aligned.sortedByCoord.out.bam" "output.STAR.1_A11_Hypo_S29_Aligned.sortedByCoord.out.bam" "output.STAR.1_A12_Hypo_S30_Aligned.sortedByCoord.out.bam" "output.STAR.1_A1_Norm_S1_Aligned.sortedByCoord.out.bam" "output.STAR.1_A2_Norm_S2_Aligned.sortedByCoord.out.bam" "output.STAR.1_A3_Norm_S3_Aligned.sortedByCoord.out.bam" "output.STAR.1_A4_Norm_S4_Aligned.sortedByCoord.out.bam" "output.STAR.1_A5_Norm_S5_Aligned.sortedByCoord.out.bam" "output.STAR.1_A6_Norm_S6_Aligned.sortedByCoord.out.bam" "output.STAR.1_A7_Hypo_S25_Aligned.sortedByCoord.out.bam" ... "output.STAR.4_H14_Hypo_S383_Aligned.sortedByCoord.out.bam" "output.STAR.4_H1_Norm_S355_Aligned.sortedByCoord.out.bam" "output.STAR.4_H2_Norm_S356_Aligned.sortedByCoord.out.bam" "output.STAR.4_H3_Norm_S357_Aligned.sortedByCoord.out.bam" "output.STAR.4_H4_Norm_S358_Aligned.sortedByCoord.out.bam" "output.STAR.4_H5_Norm_S359_Aligned.sortedByCoord.out.bam" "output.STAR.4_H6_Norm_S360_Aligned.sortedByCoord.out.bam" "output.STAR.4_H7_Hypo_S379_Aligned.sortedByCoord.out.bam" "output.STAR.4_H8_Hypo_S380_Aligned.sortedByCoord.out.bam" "output.STAR.4_H9_Hypo_S381_Aligned.sortedByCoord.out.bam"
"WASH7P" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 1 0 0 0 1 0 1
"MIR6859-1" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"WASH9P" 1 0 0 0 0 1 10 1 0 0 ... 1 1 0 0 0 0 1 1 4 5
"OR4F29" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 1 0
"MTND1P23" 0 0 0 0 0 0 0 0 0 0 ... 0 0 1 0 0 0 0 0 0 0

5 rows × 383 columns

In [ ]:
# To print the dimensions of the dataset
print("Dataframe dimensions:", np.shape(MCF7_unf))
# To display the first column of the dataset
print("First column: ", MCF7_unf.iloc[ : , 0])
Dataframe dimensions: (22934, 383)
First column:  "WASH7P"         0
"MIR6859-1"      0
"WASH9P"         1
"OR4F29"         0
"MTND1P23"       0
              ... 
"MT-TE"          4
"MT-CYB"       270
"MT-TT"          0
"MT-TP"          5
"MAFIP"          8
Name: "output.STAR.1_A10_Hypo_S28_Aligned.sortedByCoord.out.bam", Length: 22934, dtype: int64

The dimension of the MCF7 SmartSeq unfiltered data set is of 22934 rows and 383 columns.

Each column corresponds to a specific gene while each column corresponds to a cell. Hence, in each entry we can retrieve how much of tha specific genes has been expressed in that specific cell. Looking at the name of the columns we can also find directly if that cell was under normoxia or hypoxia without looking at the metadata.

In [ ]:
# To print the names
list(MCF7_unf.columns)
Out[ ]:
['"output.STAR.1_A10_Hypo_S28_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_A11_Hypo_S29_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_A12_Hypo_S30_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_A1_Norm_S1_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_A2_Norm_S2_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_A3_Norm_S3_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_A4_Norm_S4_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_A5_Norm_S5_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_A6_Norm_S6_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_A7_Hypo_S25_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_A8_Hypo_S26_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_A9_Hypo_S27_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_B10_Hypo_S76_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_B11_Hypo_S77_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_B12_Hypo_S78_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_B1_Norm_S49_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_B2_Norm_S50_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_B3_Norm_S51_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_B4_Norm_S52_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_B5_Norm_S53_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_B6_Norm_S54_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_B7_Hypo_S73_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_B8_Hypo_S74_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_B9_Hypo_S75_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_C10_Hypo_S124_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_C11_Hypo_S125_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_C12_Hypo_S126_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_C1_Norm_S97_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_C2_Norm_S98_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_C3_Norm_S99_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_C4_Norm_S100_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_C5_Norm_S101_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_C6_Norm_S102_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_C7_Hypo_S121_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_C8_Hypo_S122_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_C9_Hypo_S123_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_D10_Hypo_S172_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_D11_Hypo_S173_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_D12_Hypo_S174_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_D1_Norm_S145_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_D2_Norm_S146_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_D3_Norm_S147_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_D4_Norm_S148_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_D5_Norm_S149_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_D6_Norm_S150_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_D7_Hypo_S169_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_D8_Hypo_S170_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_D9_Hypo_S171_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_E10_Hypo_S220_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_E11_Hypo_S221_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_E12_Hypo_S222_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_E1_Norm_S193_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_E2_Norm_S194_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_E3_Norm_S195_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_E4_Norm_S196_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_E5_Norm_S197_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_E6_Norm_S198_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_E7_Hypo_S217_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_E8_Hypo_S218_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_E9_Hypo_S219_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_F10_Hypo_S268_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_F11_Hypo_S269_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_F12_Hypo_S270_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_F1_Norm_S241_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_F2_Norm_S242_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_F3_Norm_S243_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_F4_Norm_S244_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_F5_Norm_S245_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_F6_Norm_S246_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_F7_Hypo_S265_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_F8_Hypo_S266_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_F9_Hypo_S267_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_G10_Hypo_S316_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_G11_Hypo_S317_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_G12_Hypo_S318_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_G1_Norm_S289_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_G2_Norm_S290_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_G3_Norm_S291_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_G4_Norm_S292_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_G5_Norm_S293_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_G6_Norm_S294_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_G7_Hypo_S313_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_G8_Hypo_S314_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_G9_Hypo_S315_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_H10_Hypo_S364_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_H11_Hypo_S365_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_H12_Hypo_S366_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_H1_Norm_S337_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_H2_Norm_S338_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_H3_Norm_S339_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_H4_Norm_S340_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_H5_Norm_S341_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_H6_Norm_S342_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_H7_Hypo_S361_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_H8_Hypo_S362_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.1_H9_Hypo_S363_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.2_A10_Hypo_S34_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.2_A11_Hypo_S35_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.2_A12_Hypo_S36_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.2_A1_Norm_S7_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.2_A2_Norm_S8_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.2_A3_Norm_S9_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.2_A4_Norm_S10_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.2_A5_Norm_S11_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.2_A6_Norm_S12_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.2_A7_Hypo_S31_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.2_A8_Hypo_S32_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.2_A9_Hypo_S33_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.2_B10_Hypo_S82_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.2_B11_Hypo_S83_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.2_B12_Hypo_S84_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.2_B1_Norm_S55_Aligned.sortedByCoord.out.bam"',
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 '"output.STAR.4_G8_Hypo_S332_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.4_G9_Hypo_S333_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.4_H10_Hypo_S382_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.4_H14_Hypo_S383_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.4_H1_Norm_S355_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.4_H2_Norm_S356_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.4_H3_Norm_S357_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.4_H4_Norm_S358_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.4_H5_Norm_S359_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.4_H6_Norm_S360_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.4_H7_Hypo_S379_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.4_H8_Hypo_S380_Aligned.sortedByCoord.out.bam"',
 '"output.STAR.4_H9_Hypo_S381_Aligned.sortedByCoord.out.bam"']
In [ ]:
# To print the names of the genes
gene_symbls = MCF7_unf.index
print("Dataframe indexes: ", gene_symbls)
Dataframe indexes:  Index(['"WASH7P"', '"MIR6859-1"', '"WASH9P"', '"OR4F29"', '"MTND1P23"',
       '"MTND2P28"', '"MTCO1P12"', '"MTCO2P12"', '"MTATP8P1"', '"MTATP6P1"',
       ...
       '"MT-TH"', '"MT-TS2"', '"MT-TL2"', '"MT-ND5"', '"MT-ND6"', '"MT-TE"',
       '"MT-CYB"', '"MT-TT"', '"MT-TP"', '"MAFIP"'],
      dtype='object', length=22934)
In [ ]:
# To check the data types of the entries
MCF7_unf.dtypes
Out[ ]:
"output.STAR.1_A10_Hypo_S28_Aligned.sortedByCoord.out.bam"    int64
"output.STAR.1_A11_Hypo_S29_Aligned.sortedByCoord.out.bam"    int64
"output.STAR.1_A12_Hypo_S30_Aligned.sortedByCoord.out.bam"    int64
"output.STAR.1_A1_Norm_S1_Aligned.sortedByCoord.out.bam"      int64
"output.STAR.1_A2_Norm_S2_Aligned.sortedByCoord.out.bam"      int64
                                                              ...  
"output.STAR.4_H5_Norm_S359_Aligned.sortedByCoord.out.bam"    int64
"output.STAR.4_H6_Norm_S360_Aligned.sortedByCoord.out.bam"    int64
"output.STAR.4_H7_Hypo_S379_Aligned.sortedByCoord.out.bam"    int64
"output.STAR.4_H8_Hypo_S380_Aligned.sortedByCoord.out.bam"    int64
"output.STAR.4_H9_Hypo_S381_Aligned.sortedByCoord.out.bam"    int64
Length: 383, dtype: object

As shown, the genes are represented as an integer value that represents how much they are expressed in each cell

In [ ]:
# To check the null values
print(MCF7_unf.isnull().sum())
"output.STAR.1_A10_Hypo_S28_Aligned.sortedByCoord.out.bam"    0
"output.STAR.1_A11_Hypo_S29_Aligned.sortedByCoord.out.bam"    0
"output.STAR.1_A12_Hypo_S30_Aligned.sortedByCoord.out.bam"    0
"output.STAR.1_A1_Norm_S1_Aligned.sortedByCoord.out.bam"      0
"output.STAR.1_A2_Norm_S2_Aligned.sortedByCoord.out.bam"      0
                                                             ..
"output.STAR.4_H5_Norm_S359_Aligned.sortedByCoord.out.bam"    0
"output.STAR.4_H6_Norm_S360_Aligned.sortedByCoord.out.bam"    0
"output.STAR.4_H7_Hypo_S379_Aligned.sortedByCoord.out.bam"    0
"output.STAR.4_H8_Hypo_S380_Aligned.sortedByCoord.out.bam"    0
"output.STAR.4_H9_Hypo_S381_Aligned.sortedByCoord.out.bam"    0
Length: 383, dtype: int64
In [ ]:
# To remove the rows containing all 0 values
MCF7_unf2 = MCF7_unf.dropna() 
print(MCF7_unf2.isnull().sum())
# To check the dimension of the new dataset without null values
print("Dimension: ", MCF7_unf2.shape)
print("Did the dataset change?\n", not(MCF7_unf2.equals(MCF7_unf)))
"output.STAR.1_A10_Hypo_S28_Aligned.sortedByCoord.out.bam"    0
"output.STAR.1_A11_Hypo_S29_Aligned.sortedByCoord.out.bam"    0
"output.STAR.1_A12_Hypo_S30_Aligned.sortedByCoord.out.bam"    0
"output.STAR.1_A1_Norm_S1_Aligned.sortedByCoord.out.bam"      0
"output.STAR.1_A2_Norm_S2_Aligned.sortedByCoord.out.bam"      0
                                                             ..
"output.STAR.4_H5_Norm_S359_Aligned.sortedByCoord.out.bam"    0
"output.STAR.4_H6_Norm_S360_Aligned.sortedByCoord.out.bam"    0
"output.STAR.4_H7_Hypo_S379_Aligned.sortedByCoord.out.bam"    0
"output.STAR.4_H8_Hypo_S380_Aligned.sortedByCoord.out.bam"    0
"output.STAR.4_H9_Hypo_S381_Aligned.sortedByCoord.out.bam"    0
Length: 383, dtype: int64
Dimension:  (22934, 383)
Did the dataset change?
 False

After dropping the rows and the column that contains only NAs and zeroes, we see that the dataframe maintains the same dimensions. No rows or columns were dropped, the two datasets are equal.

Checking, and dropping, duplicates rows can also be usefull.

In [ ]:
# To check whether there are duplicate rows
MCF7_unf_noDup = MCF7_unf.drop_duplicates()
print("The shape without duplicates is: ", MCF7_unf_noDup.shape)
print("Did the dataset change?\n", not(MCF7_unf_noDup.equals(MCF7_unf)))
The shape without duplicates is:  (22905, 383)
Did the dataset change?
 True

Dropping the duplicate rows has changed the dimensions of the dataframe, some rows were discarded.

Let's now look at some informations about the dataframe.

In [ ]:
# To check the characteristics of each cell
MCF7_unf_describe = MCF7_unf.describe()
MCF7_unf_describe
Out[ ]:
"output.STAR.1_A10_Hypo_S28_Aligned.sortedByCoord.out.bam" "output.STAR.1_A11_Hypo_S29_Aligned.sortedByCoord.out.bam" "output.STAR.1_A12_Hypo_S30_Aligned.sortedByCoord.out.bam" "output.STAR.1_A1_Norm_S1_Aligned.sortedByCoord.out.bam" "output.STAR.1_A2_Norm_S2_Aligned.sortedByCoord.out.bam" "output.STAR.1_A3_Norm_S3_Aligned.sortedByCoord.out.bam" "output.STAR.1_A4_Norm_S4_Aligned.sortedByCoord.out.bam" "output.STAR.1_A5_Norm_S5_Aligned.sortedByCoord.out.bam" "output.STAR.1_A6_Norm_S6_Aligned.sortedByCoord.out.bam" "output.STAR.1_A7_Hypo_S25_Aligned.sortedByCoord.out.bam" ... "output.STAR.4_H14_Hypo_S383_Aligned.sortedByCoord.out.bam" "output.STAR.4_H1_Norm_S355_Aligned.sortedByCoord.out.bam" "output.STAR.4_H2_Norm_S356_Aligned.sortedByCoord.out.bam" "output.STAR.4_H3_Norm_S357_Aligned.sortedByCoord.out.bam" "output.STAR.4_H4_Norm_S358_Aligned.sortedByCoord.out.bam" "output.STAR.4_H5_Norm_S359_Aligned.sortedByCoord.out.bam" "output.STAR.4_H6_Norm_S360_Aligned.sortedByCoord.out.bam" "output.STAR.4_H7_Hypo_S379_Aligned.sortedByCoord.out.bam" "output.STAR.4_H8_Hypo_S380_Aligned.sortedByCoord.out.bam" "output.STAR.4_H9_Hypo_S381_Aligned.sortedByCoord.out.bam"
count 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 ... 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000
mean 40.817651 0.012253 86.442400 1.024636 14.531351 56.213613 75.397183 62.767725 67.396747 2.240734 ... 17.362562 42.080230 34.692422 32.735284 21.992718 17.439391 49.242784 61.545609 68.289352 62.851400
std 465.709940 0.207726 1036.572689 6.097362 123.800530 503.599145 430.471519 520.167576 459.689019 25.449630 ... 193.153757 256.775704 679.960908 300.291051 153.441647 198.179666 359.337479 540.847355 636.892085 785.670341
min 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
25% 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
50% 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
75% 17.000000 0.000000 5.000000 0.000000 7.000000 23.000000 39.000000 35.000000 38.000000 1.000000 ... 9.000000 30.000000 0.000000 17.000000 12.000000 9.000000 27.000000 30.000000 38.000000 33.000000
max 46744.000000 14.000000 82047.000000 289.000000 10582.000000 46856.000000 29534.000000 50972.000000 36236.000000 1707.000000 ... 17800.000000 23355.000000 81952.000000 29540.000000 12149.000000 19285.000000 28021.000000 40708.000000 46261.000000 68790.000000

8 rows × 383 columns

At first glance it emerges that while there are many cells with a mean greater than 40 there are many others with a mean very close to zero, hence, it seems that in these cells very few genes have been expressed. These cells could exhibit this behavior because perhaps they will probably die shortly but this is a domain specific question which we will not answer in our analysis. In any case, cells with so few expressed genes are not useful for our classification device and therefore we could delete their respective columns. Another important feature that emerges is that some cells have the max value much higher than the mean, for example in the first column the mean is equal to 40.817651 while max is equal to 46744; this makes us think that in some cells there are genes that are extremely characteristic compared to others and these genes will be the ones of greatest interest for us but it is still early to say it ...

Plotting the distribution of the mean in the cells though an histogram confirms the fact that there are two different peaks: one between 0 and 10 and the other around 50 and so the majority of the cells have a very low mean or instead one with a value near 50.

In [ ]:
# To plot an histogram with the means
sns.displot(data = MCF7_unf_describe.iloc[1], bins=50, color="teal")
plt.show()

As can be seen from the plot, the count of the means follows a bimodal distribution (with two peaks), one around 0 and the other around 50.\ Hence, already at this point, we can use a natural treshold to filter the cells where very few genes where expressed.

In [ ]:
print(MCF7_unf.shape)
data_no_zero = MCF7_unf

data_no_zero = data_no_zero.drop(columns=data_no_zero.columns[data_no_zero.describe().iloc[1]<=30])
# data_no_zero = data_no_zero.drop(data_no_zero.loc[data_no_zero.mean(axis=1)<=50].index)
# data_no_zero.describe()
(22934, 383)

We plot below the count of the means where we filtered out the cells with mean value below 30.

In [ ]:
# To plot an histogram with the means
sns.displot(data = data_no_zero.describe().iloc[1], bins=50, color="teal")
plt.show()

Another confirmation of this behaviour is given by the fact that in almost all cells the 50-percentile of the distribution is zero. Plotting instead the 75-percentile we can also see that there is a peak of cells that exibihit a 75-percentile near zero and another peak that has instead a 75-percentile near 30. Already from this basic plots we can start to formulate the hypothesis that the data at our disposal is sparse and highly not-symmetrical so we procede further is this direction.

In [ ]:
# To plot a histogram with the 75-percentile 
sns.displot(data = MCF7_unf_describe.iloc[6], bins=50, color="teal")
plt.show()

Plotting the violin plots for the first 50 samples it emerges again that there are some cells with a very short line that means that the distribution is highly concentrated near zero while the cells with a very long line are those whose tails of the distribution are 'heavy' and so there is a high probability of having data points very far from the median in this samples.

In [ ]:
# To plot a violin plot of the first 50 cells
plt.figure(figsize=(16,4))
plot=sns.violinplot(data=MCF7_unf.iloc[:, :50],palette="Set3",cut=0)
plt.setp(plot.get_xticklabels(), rotation=90)
plt.show()

To get a better visual about the distibution of genes in some specific cells, it is usefull to plot some boxplots.

In [ ]:
cnames = list(MCF7_unf.columns)
cnames[1]
sns.boxplot(x=MCF7_unf[cnames[1]])
plt.show()
In [ ]:
cnames = list(MCF7_unf.columns)
cnames[1]
sns.boxplot(x=MCF7_unf[cnames[5]])
plt.show()

We can see both from the boxplots and the violin plots that the range of the values are much different from a cell to another. But we can see that most genes have 0 value.


Here we repeat the same analysis using the transpose of the data, in order to see which genes are highly expressed with respect to others

In [ ]:
# To transpose the data
MCF7_unf_transposed = MCF7_unf.transpose()
MCF7_unf_transposed
Out[ ]:
"WASH7P" "MIR6859-1" "WASH9P" "OR4F29" "MTND1P23" "MTND2P28" "MTCO1P12" "MTCO2P12" "MTATP8P1" "MTATP6P1" ... "MT-TH" "MT-TS2" "MT-TL2" "MT-ND5" "MT-ND6" "MT-TE" "MT-CYB" "MT-TT" "MT-TP" "MAFIP"
"output.STAR.1_A10_Hypo_S28_Aligned.sortedByCoord.out.bam" 0 0 1 0 0 2 2 0 0 29 ... 0 0 0 505 147 4 270 0 5 8
"output.STAR.1_A11_Hypo_S29_Aligned.sortedByCoord.out.bam" 0 0 0 0 0 0 0 0 0 0 ... 1 1 0 1 0 0 1 0 0 0
"output.STAR.1_A12_Hypo_S30_Aligned.sortedByCoord.out.bam" 0 0 0 0 0 1 1 1 0 12 ... 0 0 0 1 0 0 76 0 0 0
"output.STAR.1_A1_Norm_S1_Aligned.sortedByCoord.out.bam" 0 0 0 0 0 0 0 0 0 7 ... 1 0 0 44 8 0 66 0 1 0
"output.STAR.1_A2_Norm_S2_Aligned.sortedByCoord.out.bam" 0 0 0 0 0 0 0 0 0 68 ... 0 0 0 237 31 3 727 0 0 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
"output.STAR.4_H5_Norm_S359_Aligned.sortedByCoord.out.bam" 0 0 0 0 0 0 1 0 0 49 ... 0 0 1 341 46 1 570 0 0 0
"output.STAR.4_H6_Norm_S360_Aligned.sortedByCoord.out.bam" 0 0 1 0 0 2 5 5 0 370 ... 0 0 2 1612 215 6 3477 3 7 6
"output.STAR.4_H7_Hypo_S379_Aligned.sortedByCoord.out.bam" 1 0 1 0 0 7 0 0 0 33 ... 0 0 0 62 20 0 349 0 2 0
"output.STAR.4_H8_Hypo_S380_Aligned.sortedByCoord.out.bam" 0 0 4 1 0 29 4 0 0 228 ... 3 0 2 1934 575 7 2184 2 28 1
"output.STAR.4_H9_Hypo_S381_Aligned.sortedByCoord.out.bam" 1 0 5 0 0 5 3 0 0 71 ... 5 2 3 1328 490 4 1149 2 11 4

383 rows × 22934 columns

In [ ]:
# To check the information about the transposed dataset
MCF7_unf_transposed_describe = MCF7_unf_transposed.describe()
MCF7_unf_transposed_describe
Out[ ]:
"WASH7P" "MIR6859-1" "WASH9P" "OR4F29" "MTND1P23" "MTND2P28" "MTCO1P12" "MTCO2P12" "MTATP8P1" "MTATP6P1" ... "MT-TH" "MT-TS2" "MT-TL2" "MT-ND5" "MT-ND6" "MT-TE" "MT-CYB" "MT-TT" "MT-TP" "MAFIP"
count 383.000000 383.000000 383.000000 383.00000 383.000000 383.000000 383.000000 383.000000 383.000000 383.000000 ... 383.000000 383.000000 383.000000 383.000000 383.000000 383.000000 383.00000 383.000000 383.000000 383.000000
mean 0.133159 0.026110 1.344648 0.05483 0.049608 6.261097 4.681462 0.524804 0.073107 222.054830 ... 1.060052 0.443864 3.146214 1016.477807 204.600522 5.049608 2374.97389 2.083551 5.626632 1.749347
std 0.618664 0.249286 2.244543 0.31477 0.229143 7.565749 6.232649 0.980857 0.298131 262.616874 ... 1.990566 1.090827 4.265352 1009.444811 220.781927 6.644302 2920.39000 3.372714 7.511180 3.895204
min 0.000000 0.000000 0.000000 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000 0.000000 0.000000
25% 0.000000 0.000000 0.000000 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000 23.000000 ... 0.000000 0.000000 0.000000 172.000000 30.500000 0.000000 216.50000 0.000000 0.000000 0.000000
50% 0.000000 0.000000 0.000000 0.00000 0.000000 3.000000 2.000000 0.000000 0.000000 98.000000 ... 0.000000 0.000000 1.000000 837.000000 152.000000 3.000000 785.00000 0.000000 3.000000 0.000000
75% 0.000000 0.000000 2.000000 0.00000 0.000000 10.000000 7.000000 1.000000 0.000000 370.500000 ... 1.000000 0.000000 5.000000 1549.000000 294.000000 7.000000 4059.00000 3.000000 8.000000 2.000000
max 9.000000 4.000000 20.000000 3.00000 2.000000 45.000000 36.000000 6.000000 2.000000 1662.000000 ... 15.000000 8.000000 22.000000 8115.000000 2002.000000 46.000000 16026.00000 22.000000 56.000000 32.000000

8 rows × 22934 columns

In [ ]:
# to plot a histogram with the mean of the expression of the genes
sns.displot(data = MCF7_unf_transposed_describe.iloc[1], bins=500, color="teal")
# we limit the x axis since most of the values are around 0
plt.xlim(0, 600)
plt.show()

From this plot it is simple to see that most of the genes are not present in most of the cells. The same can be seen for the 75% percetile.

In [ ]:
# to plot a histogram with the 75% percentile of the expression of the genes
sns.displot(data = MCF7_unf_transposed_describe.iloc[6], bins=500, color="teal")
# we limit the x axis since most of the values are around 0
plt.xlim(0, 1000)
plt.show()

From this plots we can deduce that specific genes are not expressed in most of the cells.

In [ ]:
# To plot a violin plot of the first 50 genes
df_small = MCF7_unf_transposed_describe.iloc[:, :50]
plt.figure(figsize=(16,4))
plot=sns.violinplot(data=df_small,palette="Set3",cut=0)
plt.setp(plot.get_xticklabels(), rotation=90)
plt.show()

Also the violin plots show that most of the probability of a gene to be near the 0 values is much higher than any other value.

Correlation

In order to understand if there are some genes that are highly correlated we plot che a table with the correlation of the first 25 genes.

In [ ]:
# To see the correlation between genes
df_new = MCF7_unf.transpose().iloc[:,:25]
plt.figure(figsize=(25,25))
sns.heatmap(df_new.corr(),cbar=True,annot=True,cmap='Blues')
plt.show()

From the table we deduce that the genes interact between them in a quite complex way: some are positively correlated while others are negatively correlated. Interestingly there are some genes that have a very high correlation; this could mean that they are the same gene or they are genes with a very high level of similarity.


Outliers

We can now look for outliers. And let's try to eliminate them and look again at the violin plots.

In [ ]:
# To find interquartile range
Q1 = MCF7_unf.quantile(0.25)
Q3 = MCF7_unf.quantile(0.75)
IQR = Q3 - Q1
print(IQR)
"output.STAR.1_A10_Hypo_S28_Aligned.sortedByCoord.out.bam"    17.0
"output.STAR.1_A11_Hypo_S29_Aligned.sortedByCoord.out.bam"     0.0
"output.STAR.1_A12_Hypo_S30_Aligned.sortedByCoord.out.bam"     5.0
"output.STAR.1_A1_Norm_S1_Aligned.sortedByCoord.out.bam"       0.0
"output.STAR.1_A2_Norm_S2_Aligned.sortedByCoord.out.bam"       7.0
                                                              ... 
"output.STAR.4_H5_Norm_S359_Aligned.sortedByCoord.out.bam"     9.0
"output.STAR.4_H6_Norm_S360_Aligned.sortedByCoord.out.bam"    27.0
"output.STAR.4_H7_Hypo_S379_Aligned.sortedByCoord.out.bam"    30.0
"output.STAR.4_H8_Hypo_S380_Aligned.sortedByCoord.out.bam"    38.0
"output.STAR.4_H9_Hypo_S381_Aligned.sortedByCoord.out.bam"    33.0
Length: 383, dtype: float64
In [ ]:
# To find values in the interquartile range
df_noOut = MCF7_unf[~((MCF7_unf < (Q1 - 1.5 * IQR)) |(MCF7_unf > (Q3 + 1.5 * IQR))).any(axis=1)]
df_noOut.shape
df_noOut.head(3)
Out[ ]:
"output.STAR.1_A10_Hypo_S28_Aligned.sortedByCoord.out.bam" "output.STAR.1_A11_Hypo_S29_Aligned.sortedByCoord.out.bam" "output.STAR.1_A12_Hypo_S30_Aligned.sortedByCoord.out.bam" "output.STAR.1_A1_Norm_S1_Aligned.sortedByCoord.out.bam" "output.STAR.1_A2_Norm_S2_Aligned.sortedByCoord.out.bam" "output.STAR.1_A3_Norm_S3_Aligned.sortedByCoord.out.bam" "output.STAR.1_A4_Norm_S4_Aligned.sortedByCoord.out.bam" "output.STAR.1_A5_Norm_S5_Aligned.sortedByCoord.out.bam" "output.STAR.1_A6_Norm_S6_Aligned.sortedByCoord.out.bam" "output.STAR.1_A7_Hypo_S25_Aligned.sortedByCoord.out.bam" ... "output.STAR.4_H14_Hypo_S383_Aligned.sortedByCoord.out.bam" "output.STAR.4_H1_Norm_S355_Aligned.sortedByCoord.out.bam" "output.STAR.4_H2_Norm_S356_Aligned.sortedByCoord.out.bam" "output.STAR.4_H3_Norm_S357_Aligned.sortedByCoord.out.bam" "output.STAR.4_H4_Norm_S358_Aligned.sortedByCoord.out.bam" "output.STAR.4_H5_Norm_S359_Aligned.sortedByCoord.out.bam" "output.STAR.4_H6_Norm_S360_Aligned.sortedByCoord.out.bam" "output.STAR.4_H7_Hypo_S379_Aligned.sortedByCoord.out.bam" "output.STAR.4_H8_Hypo_S380_Aligned.sortedByCoord.out.bam" "output.STAR.4_H9_Hypo_S381_Aligned.sortedByCoord.out.bam"
"MIR6859-1" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"CICP3" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"FAM87B" 0 0 0 0 0 0 0 0 2 0 ... 0 1 0 0 0 0 0 0 0 0

3 rows × 383 columns

In [ ]:
sns.boxplot(x=df_noOut[cnames[1]])
plt.show()
In [ ]:
df_noOut_small = df_noOut.iloc[:, :50]
plt.figure(figsize=(16,4))
plot=sns.violinplot(data=df_noOut_small,palette="Set3",cut=0)
plt.setp(plot.get_xticklabels(), rotation=90)
plt.show()

As seen from the data, most of the genes are expressed in the last quartile. Hence, in this case, the outliers carry most of the information and by removing them we would lose a great part of it. That is due to the fact that the data is sparse, and that makes it harder to just exclude outliers from the dataset.

Sparsity

We have tried to quantify the sparsity using an index given by the difference between 1 and the ratio of nonzero values and the size of the data set. This tells us that around 60% of the data is 0, hence highly sparse.

In [ ]:
# create a 2-D representation of the matrix
MCF7_arr = np.array(MCF7_unf)
print("Dense matrix representation: \n", MCF7_arr)
Dense matrix representation: 
 [[ 0  0  0 ...  1  0  1]
 [ 0  0  0 ...  0  0  0]
 [ 1  0  0 ...  1  4  5]
 ...
 [ 0  0  0 ...  0  2  2]
 [ 5  0  0 ...  2 28 11]
 [ 8  0  0 ...  0  1  4]]
In [ ]:
# calculate sparsity
sparsity = 1.0 - count_nonzero(MCF7_arr) / MCF7_arr.size
print(sparsity)
0.6021531646834907

From here we can deduce that around 60% of the data is equal to zero.

Therefore, we tried to represent the data set as a sparse matrix using the csr_matrix() function, and analysed the differences in memory storage between the two representations. In practice, the original numpy array takes almost the double of the storage compared to the sparse matrix, that is why this representation can be an advantage.

In [ ]:
# convert to sparse matrix representation 
S = csr_matrix(MCF7_arr)
print("Sparse matrix: \n",S)
Sparse matrix: 
   (0, 20)	1
  (0, 49)	1
  (0, 72)	1
  (0, 85)	1
  (0, 106)	2
  (0, 126)	1
  (0, 127)	1
  (0, 133)	2
  (0, 158)	9
  (0, 166)	1
  (0, 170)	1
  (0, 171)	1
  (0, 186)	1
  (0, 189)	3
  (0, 195)	1
  (0, 199)	2
  (0, 209)	1
  (0, 210)	1
  (0, 218)	1
  (0, 228)	2
  (0, 235)	1
  (0, 270)	4
  (0, 276)	1
  (0, 292)	1
  (0, 314)	2
  :	:
  (22933, 334)	12
  (22933, 336)	2
  (22933, 337)	1
  (22933, 340)	2
  (22933, 341)	3
  (22933, 342)	1
  (22933, 345)	3
  (22933, 346)	1
  (22933, 347)	6
  (22933, 348)	5
  (22933, 350)	5
  (22933, 351)	5
  (22933, 352)	1
  (22933, 357)	1
  (22933, 358)	6
  (22933, 361)	4
  (22933, 363)	2
  (22933, 369)	1
  (22933, 371)	2
  (22933, 372)	1
  (22933, 376)	2
  (22933, 377)	1
  (22933, 379)	6
  (22933, 381)	1
  (22933, 382)	4
In [ ]:
# To calculate the memory usage of the original dataset
print('MCF7_arr.nbytes: {0} bytes'.format(MCF7_arr.nbytes))
print('sys.getsizeof(MCF7_arr): {0} bytes'.format(sys.getsizeof(MCF7_arr)))
MCF7_arr.nbytes: 70269776 bytes
sys.getsizeof(MCF7_arr): 70269896 bytes
In [ ]:
# To calculate the memory usage of the sparse matrix
S.data.nbytes + S.indptr.nbytes + S.indices.nbytes
Out[ ]:
42026652
In [ ]:
# convert back to 2-D representation of the matrix
B = S.todense()
print("Dense matrix: \n", B)
Dense matrix: 
 [[ 0  0  0 ...  1  0  1]
 [ 0  0  0 ...  0  0  0]
 [ 1  0  0 ...  1  4  5]
 ...
 [ 0  0  0 ...  0  2  2]
 [ 5  0  0 ...  2 28 11]
 [ 8  0  0 ...  0  1  4]]
In [ ]:
B.nbytes
Out[ ]:
70269776

We're happy to see that the sparse matrix occupy less space than the original data (without loosing any information)


Checking the Normality

We then analysed the skewness and Kurtosis of a single cell of the data to check whether it is normalised, but because most of these values are not near 0, we can deduce that most of the cells have a distribution that differ much from the normal one.\

In [ ]:
#np.sum(MCF7_unf_sum.iloc[4] != 0)
MCF7_noOut = MCF7_unf
In [ ]:
cnames = MCF7_unf.columns
In [ ]:
# To calculate the skewness
from scipy.stats import kurtosis, skew
from sklearn.preprocessing import PowerTransformer, QuantileTransformer

colN = np.shape(MCF7_unf)[1]
colN
df_skew_cells = []
for i in range(colN) :     
     v_df = MCF7_unf[cnames[i]]
     df_skew_cells += [skew(v_df)]   
  #  df_skew_cells += [df[cnames[i]].skew()]
df_skew_cells

plt.figure(figsize=(10,7))
sns.histplot(df_skew_cells, bins=100, color="teal")
plt.xlabel('Skewness of single cells expression profiles - original df')
plt.show()
In [ ]:
# To calculate the kurtosis
df_kurt_cells = []
for i in range(colN) :     
     v_df = MCF7_unf[cnames[i]]
     df_kurt_cells += [kurtosis(v_df)]   
 #   df_kurt_cells += [df[cnames[i]].kurt()]
df_kurt_cells

plt.figure(figsize=(10,7))
sns.histplot(df_kurt_cells, bins=100, color="teal")
plt.xlabel('Kurtosis of single cells expression profiles - original df')
plt.show()
In [ ]:
# To check normality of the genes
df_small = MCF7_unf.transpose().iloc[:, 10:30]  #just selecting part of the samples so run time not too long
plt.figure(figsize=(10,7))
sns.displot(data=df_small,palette="Set3",kind="kde", bw_adjust=2)
plt.show()
<Figure size 720x504 with 0 Axes>

To show that the normality assumption is not satisfied we the qqplot() function.

In [ ]:
# QQ Plot
from numpy.random import seed
from numpy.random import randn
from statsmodels.graphics.gofplots import qqplot
# seed the random number generator
seed(1)
# generate univariate observations
data = 5 * randn(100) + 50
# q-q plot
qqplot(MCF7_unf, line='s')
plt.show()

We compare the QQplot in the filtered and normalized case:

In [ ]:
# QQ Plot
from numpy.random import seed
from numpy.random import randn
from statsmodels.graphics.gofplots import qqplot
# seed the random number generator
seed(1)
# generate univariate observations
data = 5 * randn(100) + 50
# q-q plot
qqplot(MCF7_f_n, line='s')
plt.show()

In reality, it's very unlikely to find data that are normally distributed. Also in this case, as we can see by plotting the QQ-plot, the data are not normally distributed, in fact, the data points in the plot are not close to the red line.

Another approach we took was to try to filter the data by dropping all the rows (genes) that have third quantile smaller than 95 and by dropping the columns (cells) that have third quantile smaller than 14. These two numbers allows us to get a dataset that has dimensions similar to the ones of the filtered and normalized dataset. Unfortunately, they do not coincide.

In [ ]:
data = MCF7_unf
data_d = data.T.describe()
In [ ]:
data_d_n = data.describe()
In [ ]:
data1 = data.drop(data.loc[data_d.iloc[6]<=95].index)
print(data1.shape)
data2 = data1.drop(columns=data1.columns[data_d_n.iloc[6]<=14])
print(data2.shape)
print(len([i for i in list(MCF7_f_n.index) if i in list(data2.index)]))
#print(data2)
(3032, 383)
(3032, 252)
544
Log_2

We can now try to compute the log_2 of all the dataset, after adding 1 to it (do don't have problems with the zeros), and see if it can be a good normalization by looking again to the plot of the skenwness and the kurtosis.

In [ ]:
MCF7_unf_plus = MCF7_unf + 1
MCF7_unf_log2 = MCF7_unf_plus.apply(np.log2)
MCF7_unf_log2.describe()
Out[ ]:
"output.STAR.1_A10_Hypo_S28_Aligned.sortedByCoord.out.bam" "output.STAR.1_A11_Hypo_S29_Aligned.sortedByCoord.out.bam" "output.STAR.1_A12_Hypo_S30_Aligned.sortedByCoord.out.bam" "output.STAR.1_A1_Norm_S1_Aligned.sortedByCoord.out.bam" "output.STAR.1_A2_Norm_S2_Aligned.sortedByCoord.out.bam" "output.STAR.1_A3_Norm_S3_Aligned.sortedByCoord.out.bam" "output.STAR.1_A4_Norm_S4_Aligned.sortedByCoord.out.bam" "output.STAR.1_A5_Norm_S5_Aligned.sortedByCoord.out.bam" "output.STAR.1_A6_Norm_S6_Aligned.sortedByCoord.out.bam" "output.STAR.1_A7_Hypo_S25_Aligned.sortedByCoord.out.bam" ... "output.STAR.4_H14_Hypo_S383_Aligned.sortedByCoord.out.bam" "output.STAR.4_H1_Norm_S355_Aligned.sortedByCoord.out.bam" "output.STAR.4_H2_Norm_S356_Aligned.sortedByCoord.out.bam" "output.STAR.4_H3_Norm_S357_Aligned.sortedByCoord.out.bam" "output.STAR.4_H4_Norm_S358_Aligned.sortedByCoord.out.bam" "output.STAR.4_H5_Norm_S359_Aligned.sortedByCoord.out.bam" "output.STAR.4_H6_Norm_S360_Aligned.sortedByCoord.out.bam" "output.STAR.4_H7_Hypo_S379_Aligned.sortedByCoord.out.bam" "output.STAR.4_H8_Hypo_S380_Aligned.sortedByCoord.out.bam" "output.STAR.4_H9_Hypo_S381_Aligned.sortedByCoord.out.bam"
count 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 ... 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000 22934.000000
mean 1.889979 0.009665 1.732075 0.408770 1.563776 2.174915 2.539393 2.600671 2.502254 0.627249 ... 1.659217 2.371224 0.511852 1.972339 1.744485 1.624858 2.145188 2.221317 2.368192 2.298742
std 2.743667 0.115893 3.060936 0.932712 2.158735 2.936550 3.166716 3.027012 3.107430 1.184292 ... 2.207388 2.864281 1.880059 2.656387 2.428364 2.241559 2.939852 2.998384 3.098435 2.993186
min 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
25% 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
50% 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
75% 4.169925 0.000000 2.584963 0.000000 3.000000 4.584963 5.321928 5.169925 5.285402 1.000000 ... 3.321928 4.954196 0.000000 4.169925 3.700440 3.321928 4.807355 4.954196 5.285402 5.087463
max 15.512524 3.906891 16.324181 8.179909 13.369461 15.515977 14.850138 15.637446 15.145176 10.738092 ... 14.119671 14.511506 16.322509 14.850431 13.568669 14.235266 14.774272 15.313060 15.497540 16.069932

8 rows × 383 columns

Histogram of the mean

In [ ]:
# To plot an histogram with the means
sns.displot(data = MCF7_unf_log2.describe().iloc[1], bins=50, color="teal")
plt.show()

Histogram of the third quantile

In [ ]:
# To plot an histogram with the third quantile
sns.displot(data = MCF7_unf_log2.describe().iloc[6], bins=50, color="teal")
plt.show()

We can see that we still have many zeroes, but way less than before. We have also a much smaller range of values.

Let's now plot again the skeness and the curtosis of the cells, but of the dataset where we pwerformed the logarithms.

In [ ]:
cnames = MCF7_unf_log2.columns
In [ ]:
# To calculate the skewness
from scipy.stats import kurtosis, skew

colN = np.shape(MCF7_unf_log2)[1]
colN
df_skew_cells = []
for i in range(colN) :     
     v_df = MCF7_unf_log2[cnames[i]]
     df_skew_cells += [skew(v_df)]   
  #  df_skew_cells += [df[cnames[i]].skew()]
df_skew_cells

plt.figure(figsize=(10,7))
sns.histplot(df_skew_cells, bins=100, color="teal")
plt.xlabel('Skewness of single cells expression profiles - log_2 df')
plt.show()
In [ ]:
# To calculate the kurtosis
df_kurt_cells = []
for i in range(colN) :     
     v_df = MCF7_unf_log2[cnames[i]]
     df_kurt_cells += [kurtosis(v_df)]   
 #   df_kurt_cells += [df[cnames[i]].kurt()]
df_kurt_cells

plt.figure(figsize=(10,7))
sns.histplot(df_kurt_cells, bins=100, color="teal")
plt.xlabel('Kurtosis of single cells expression profiles - log_2 df')
plt.show()

We can definetely see that the data is much more normalized because most of the skewnwss and curtosis (not of all cells but most) is equal to 0.

HCC1806

We continue by analyzing the HCC1806 dataset.

Understanding the data
In [ ]:
print("Dataframe dimensions:", np.shape(HCC1806_unf))
print("First column: ", HCC1806_unf.iloc[ : , 0])
Dataframe dimensions: (23396, 243)
First column:  "WASH7P"         0
"CICP27"         0
"DDX11L17"       0
"WASH9P"         0
"OR4F29"         2
              ... 
"MT-TE"         22
"MT-CYB"      4208
"MT-TT"         26
"MT-TP"         66
"MAFIP"          0
Name: "output.STAR.PCRPlate1A10_Normoxia_S123_Aligned.sortedByCoord.out.bam", Length: 23396, dtype: int64

Let's now look at some informations about the dataframe.

In [ ]:
# To check the characteristics of each cell
HCC1806_unf_describe = HCC1806_unf.describe()
HCC1806_unf_describe
Out[ ]:
"output.STAR.PCRPlate1A10_Normoxia_S123_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A12_Normoxia_S26_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A1_Hypoxia_S97_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A2_Hypoxia_S104_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A3_Hypoxia_S4_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A4_Hypoxia_S8_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A5_Hypoxia_S108_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A6_Hypoxia_S11_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A7_Normoxia_S113_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A8_Normoxia_S119_Aligned.sortedByCoord.out.bam" ... "output.STAR.PCRPlate4G12_Normoxia_S243_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G1_Hypoxia_S193_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G2_Hypoxia_S198_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G6_Hypoxia_S232_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G7_Normoxia_S204_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H10_Normoxia_S210_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H11_Normoxia_S214_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H2_Hypoxia_S199_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H7_Normoxia_S205_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H9_Normoxia_S236_Aligned.sortedByCoord.out.bam"
count 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 ... 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000
mean 99.565695 207.678278 9.694734 150.689007 35.700504 47.088434 152.799453 135.869422 38.363908 45.512139 ... 76.361771 105.566593 54.026116 29.763806 28.905411 104.740725 35.181569 108.197940 37.279962 76.303855
std 529.532443 981.107905 65.546050 976.936548 205.885369 545.367706 864.974182 870.729740 265.062493 366.704721 ... 346.659348 536.881574 344.068304 186.721266 135.474736 444.773045 170.872090 589.082268 181.398951 369.090274
min 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
25% 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
50% 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... 1.000000 0.000000 0.000000 0.000000 0.000000 2.000000 0.000000 0.000000 0.000000 1.000000
75% 51.000000 125.000000 5.000000 40.000000 22.000000 17.000000 81.000000 76.000000 22.000000 18.000000 ... 56.000000 67.000000 29.000000 18.000000 19.000000 76.000000 24.000000 68.000000 22.000000 44.000000
max 35477.000000 69068.000000 6351.000000 70206.000000 17326.000000 47442.000000 43081.000000 62813.000000 30240.000000 35450.000000 ... 19629.000000 30987.000000 21894.000000 13457.000000 11488.000000 33462.000000 15403.000000 34478.000000 10921.000000 28532.000000

8 rows × 243 columns

As in the MCF7 dataset, a feature that emerges is that some cells have the max value much higher than the mean, for example in the first column the mean is equal to 99.565695 while max is equal to 35477; this makes us think that in some cells there are genes that are extremely characteristic compared to others and these genes will be the ones of greatest interest for us but it is still early to say it ...

Plotting the count of the means in the cells through an histogram confirms the fact that there are several peaks, the greatest one being at around 45. The data is dishomogeneus.

In [ ]:
# To plot an histogram with the means
sns.displot(HCC1806_unf_describe.iloc[1], bins=50, color="teal")
plt.show()

We can see that, differently than the MCF7 dataframe, less cells have mean of genes equal to 0.\ By plotting the third quantile, it can be seen that there is a peak at around 25.\ Much more interesting is the fact that, in general, it seems that the average 75% quantile is smaller than the mean. This is probably due to the fact that we have many cells with 0-value.

In [ ]:
# To plot a histogram with the 75-percentile
sns.displot(data = HCC1806_unf_describe.iloc[6], bins=50, color="teal")
plt.show()

Plotting the violin plots for the first 50 samples it emerges again that there are some cells with a very short line that means that the distribution is highly concentrated near zero while the cells with a very long line are those whose tails of the distribution are 'heavy' and so there is a high probability of having data points very far from the median in this samples.

In [ ]:
# To plot a violin plot of the first 50 cells
plt.figure(figsize=(16,4))
plot=sns.violinplot(data=HCC1806_unf.iloc[:, :50],palette="Set3",cut=0)
plt.setp(plot.get_xticklabels(), rotation=90)
plt.show()

To get a better visual about the distibution of genes in some specific cells, it is usefull to plot some boxplots.

In [ ]:
cnames = list(HCC1806_unf.columns)
cnames[1]
sns.boxplot(x=HCC1806_unf[cnames[1]])
plt.show()
In [ ]:
cnames = list(HCC1806_unf.columns)
cnames[1]
sns.boxplot(x=HCC1806_unf[cnames[5]])
plt.show()

We can see both from the boxplots and the violin plots that the range of the values are much different from a cell to another. But we can see that most genes have 0 value.


Here we repeat the same analysis using the transpose of the data, in order to see which genes are highly expressed with respect to others

In [ ]:
# To transpose the data
HCC1806_unf_transposed = HCC1806_unf.transpose()
HCC1806_unf_transposed
Out[ ]:
"WASH7P" "CICP27" "DDX11L17" "WASH9P" "OR4F29" "MTND1P23" "MTND2P28" "MTCO1P12" "MTCO2P12" "MTATP8P1" ... "MT-TH" "MT-TS2" "MT-TL2" "MT-ND5" "MT-ND6" "MT-TE" "MT-CYB" "MT-TT" "MT-TP" "MAFIP"
"output.STAR.PCRPlate1A10_Normoxia_S123_Aligned.sortedByCoord.out.bam" 0 0 0 0 2 250 54 1740 6 1 ... 17 5 15 3852 900 22 4208 26 66 0
"output.STAR.PCRPlate1A12_Normoxia_S26_Aligned.sortedByCoord.out.bam" 0 0 0 0 0 424 100 2340 5 1 ... 49 29 36 7457 1439 43 6491 62 71 4
"output.STAR.PCRPlate1A1_Hypoxia_S97_Aligned.sortedByCoord.out.bam" 0 0 0 0 0 11 0 22 0 0 ... 0 0 0 93 12 0 25 0 1 0
"output.STAR.PCRPlate1A2_Hypoxia_S104_Aligned.sortedByCoord.out.bam" 0 0 0 0 0 63 16 1020 3 0 ... 43 17 8 1479 234 0 4819 11 3 7
"output.STAR.PCRPlate1A3_Hypoxia_S4_Aligned.sortedByCoord.out.bam" 0 0 0 0 0 27 3 303 0 0 ... 0 0 3 303 33 0 310 4 9 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
"output.STAR.PCRPlate4H10_Normoxia_S210_Aligned.sortedByCoord.out.bam" 0 0 0 1 0 146 47 961 1 0 ... 25 17 11 2926 423 26 3719 42 48 3
"output.STAR.PCRPlate4H11_Normoxia_S214_Aligned.sortedByCoord.out.bam" 0 0 0 0 0 37 6 372 0 0 ... 2 1 3 688 114 1 984 1 18 0
"output.STAR.PCRPlate4H2_Hypoxia_S199_Aligned.sortedByCoord.out.bam" 0 0 0 1 0 83 30 1128 4 0 ... 9 6 23 2999 486 4 2256 15 36 2
"output.STAR.PCRPlate4H7_Normoxia_S205_Aligned.sortedByCoord.out.bam" 0 0 0 0 0 47 7 258 1 0 ... 2 3 3 611 75 4 981 6 8 1
"output.STAR.PCRPlate4H9_Normoxia_S236_Aligned.sortedByCoord.out.bam" 0 0 0 0 0 249 38 980 0 0 ... 14 3 15 2460 513 20 2039 34 79 5

243 rows × 23396 columns

In [ ]:
# To check the information about the transposed dataset
HCC1806_unf_transposed_describe = HCC1806_unf_transposed.describe()
HCC1806_unf_transposed_describe
Out[ ]:
"WASH7P" "CICP27" "DDX11L17" "WASH9P" "OR4F29" "MTND1P23" "MTND2P28" "MTCO1P12" "MTCO2P12" "MTATP8P1" ... "MT-TH" "MT-TS2" "MT-TL2" "MT-ND5" "MT-ND6" "MT-TE" "MT-CYB" "MT-TT" "MT-TP" "MAFIP"
count 243.000000 243.000000 243.000000 243.000000 243.000000 243.000000 243.000000 243.000000 243.000000 243.000000 ... 243.000000 243.000000 243.000000 243.000000 243.000000 243.000000 243.000000 243.000000 243.000000 243.000000
mean 0.045267 0.119342 0.469136 0.255144 0.127572 117.930041 28.427984 904.308642 1.403292 0.378601 ... 10.358025 5.930041 13.493827 2290.213992 386.901235 18.246914 2163.588477 20.613169 46.444444 3.897119
std 0.318195 0.594531 1.455282 0.818639 0.440910 103.038022 26.062662 654.520308 1.735003 0.747361 ... 10.910199 7.040559 11.803967 1726.423259 309.276105 54.076514 1730.393947 22.224590 47.684223 4.736193
min 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
25% 0.000000 0.000000 0.000000 0.000000 0.000000 46.500000 8.000000 390.500000 0.000000 0.000000 ... 2.000000 1.000000 4.000000 918.000000 138.500000 4.000000 947.500000 5.000000 14.000000 0.000000
50% 0.000000 0.000000 0.000000 0.000000 0.000000 94.000000 22.000000 790.000000 1.000000 0.000000 ... 7.000000 4.000000 10.000000 1848.000000 320.000000 11.000000 1774.000000 14.000000 38.000000 2.000000
75% 0.000000 0.000000 0.000000 0.000000 0.000000 157.000000 42.000000 1208.000000 2.000000 1.000000 ... 14.000000 7.500000 20.000000 3172.000000 528.000000 20.000000 2927.000000 30.500000 64.500000 6.000000
max 3.000000 5.000000 12.000000 6.000000 4.000000 694.000000 120.000000 3569.000000 12.000000 4.000000 ... 52.000000 43.000000 57.000000 8972.000000 1439.000000 804.000000 11383.000000 154.000000 409.000000 24.000000

8 rows × 23396 columns

In [ ]:
# to plot a histogram with the mean of the expression of the genes
sns.displot(data = HCC1806_unf_transposed_describe.iloc[1], bins=500)
# we limit the x axis becuase most of the value is near 0
plt.xlim(0, 1000)
plt.show()

From this plot it is simple to see that most of the genes are not present in most of the cells. The same can be seen for the 75% percetile.

In [ ]:
# to plot a histogram with the 75% of the expression of the genes
sns.displot(data = HCC1806_unf_transposed_describe.iloc[6], bins=500)
# we limit the x axis becuase most of the value is near 0
plt.xlim(0, 1000)
plt.show()

From these plots we can deduce that specific genes are not expressed in most of the cells.

In [ ]:
# To plot a violin plot of the first 50 genes
df_small = HCC1806_unf_transposed_describe.iloc[:, :50]
plt.figure(figsize=(16,4))
plot=sns.violinplot(data=df_small,palette="Set3",cut=0)
plt.setp(plot.get_xticklabels(), rotation=90)
plt.show()

Also the violin plots show us that the probability of a gene to be near the 0 values in most cells is much higher than any other probability.

Correlation
In [ ]:
# To see the correlation between genes
df_new = HCC1806_unf.transpose().iloc[:,:25]
plt.figure(figsize=(25,25))
sns.heatmap(df_new.corr(),cbar=True,annot=True,cmap='Blues')
plt.show()
Outliners

Let's now look for outliners. and let's try to eliminate them and look at the violin plots./ We first find the interquartile range of the data by eliminating the first and last quantile.

In [ ]:
# To find interquartile range
Q1 = HCC1806_unf.quantile(0.25)
Q3 = HCC1806_unf.quantile(0.75)
IQR = Q3 - Q1
print(IQR)
"output.STAR.PCRPlate1A10_Normoxia_S123_Aligned.sortedByCoord.out.bam"     51.0
"output.STAR.PCRPlate1A12_Normoxia_S26_Aligned.sortedByCoord.out.bam"     125.0
"output.STAR.PCRPlate1A1_Hypoxia_S97_Aligned.sortedByCoord.out.bam"         5.0
"output.STAR.PCRPlate1A2_Hypoxia_S104_Aligned.sortedByCoord.out.bam"       40.0
"output.STAR.PCRPlate1A3_Hypoxia_S4_Aligned.sortedByCoord.out.bam"         22.0
                                                                          ...  
"output.STAR.PCRPlate4H10_Normoxia_S210_Aligned.sortedByCoord.out.bam"     76.0
"output.STAR.PCRPlate4H11_Normoxia_S214_Aligned.sortedByCoord.out.bam"     24.0
"output.STAR.PCRPlate4H2_Hypoxia_S199_Aligned.sortedByCoord.out.bam"       68.0
"output.STAR.PCRPlate4H7_Normoxia_S205_Aligned.sortedByCoord.out.bam"      22.0
"output.STAR.PCRPlate4H9_Normoxia_S236_Aligned.sortedByCoord.out.bam"      44.0
Length: 243, dtype: float64
In [ ]:
# To find values in the interquartile range
df_noOut = HCC1806_unf[~((HCC1806_unf < (Q1 - 1.5 * IQR)) |(HCC1806_unf > (Q3 + 1.5 * IQR))).any(axis=1)]
df_noOut.shape
df_noOut.head(3)
Out[ ]:
"output.STAR.PCRPlate1A10_Normoxia_S123_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A12_Normoxia_S26_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A1_Hypoxia_S97_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A2_Hypoxia_S104_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A3_Hypoxia_S4_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A4_Hypoxia_S8_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A5_Hypoxia_S108_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A6_Hypoxia_S11_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A7_Normoxia_S113_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A8_Normoxia_S119_Aligned.sortedByCoord.out.bam" ... "output.STAR.PCRPlate4G12_Normoxia_S243_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G1_Hypoxia_S193_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G2_Hypoxia_S198_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G6_Hypoxia_S232_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G7_Normoxia_S204_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H10_Normoxia_S210_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H11_Normoxia_S214_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H2_Hypoxia_S199_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H7_Normoxia_S205_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H9_Normoxia_S236_Aligned.sortedByCoord.out.bam"
"WASH7P" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"CICP27" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"DDX11L17" 0 0 0 0 0 1 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0

3 rows × 243 columns

In [ ]:
cnames = df_noOut.columns
sns.boxplot(x=df_noOut[cnames[1]])
plt.show()
In [ ]:
df_noOut_small = df_noOut.iloc[:, :50]
plt.figure(figsize=(16,4))
plot=sns.violinplot(data=df_noOut_small,palette="Set3",cut=0)
plt.setp(plot.get_xticklabels(), rotation=90)
plt.show()

As seen from the data, most of the genes are expressed in the last quartile. Hence, in this case, the outliers carry most of the information and by removing them we would lose a great part of it. That is due to the fact that the data is sparse, and that makes it harder to just exclude outliers from the dataset.

Sparsity

We have tried to quantify the sparsity using an index given by the difference between 1 and the ratio of nonzero values and the size of the data set. This tells us that around 60% of the data is 0, hence highly sparse.

In [ ]:
# create a 2-D representation of the matrix
HCC1806_arr = np.array(HCC1806_unf)
print("Dense matrix representation: \n", HCC1806_arr)
Dense matrix representation: 
 [[ 0  0  0 ...  0  0  0]
 [ 0  0  0 ...  0  0  0]
 [ 0  0  0 ...  0  0  0]
 ...
 [26 62  0 ... 15  6 34]
 [66 71  1 ... 36  8 79]
 [ 0  4  0 ...  2  1  5]]
In [ ]:
# calculate sparsity
sparsity = 1.0 - count_nonzero(HCC1806_arr) / HCC1806_arr.size
print(sparsity)
0.558456230779135

From here we can deduce that around 56% of the data is equal to zero.

Checking the Normality

We then analysed the skewness and Kurtosis of a single cell of the data to check whether it is normalised, but because most of these values are not near 0, we can deduce that most of the cells have a distribution that differ much from the normal one.\

In [ ]:
#np.sum(MCF7_unf_sum.iloc[4] != 0)
HCC1806_noOut = HCC1806_unf
In [ ]:
cnames = HCC1806_unf.columns
In [ ]:
# To calculate the skewness
from scipy.stats import kurtosis, skew
from sklearn.preprocessing import PowerTransformer, QuantileTransformer

colN = np.shape(HCC1806_unf)[1]
colN
df_skew_cells = []
for i in range(colN) :     
     v_df = HCC1806_unf[cnames[i]]
     df_skew_cells += [skew(v_df)]   
  #  df_skew_cells += [df[cnames[i]].skew()]
df_skew_cells

plt.figure(figsize=(10,7))
sns.histplot(df_skew_cells, bins=100, color="teal")
plt.xlabel('Skewness of single cells expression profiles - original df')
plt.show()
In [ ]:
# To calculate the kurtosis
df_kurt_cells = []
for i in range(colN) :     
     v_df = HCC1806_unf[cnames[i]]
     df_kurt_cells += [kurtosis(v_df)]   
 #   df_kurt_cells += [df[cnames[i]].kurt()]
df_kurt_cells

plt.figure(figsize=(10,7))
sns.histplot(df_kurt_cells, bins=100, color="teal")
plt.xlabel('Kurtosis of single cells expression profiles - original df')
plt.show()
In [ ]:
# To check normality of the genes
df_small = HCC1806_unf.transpose().iloc[:, 10:30]  #just selecting part of the samples so run time not too long
plt.figure(figsize=(10,7))
sns.displot(data=df_small,palette="Set3",kind="kde", bw_adjust=2)
plt.show()
<Figure size 720x504 with 0 Axes>

To show that the normality assumption is not satisfied we the qqplot() function.

In [ ]:
# QQ Plot
from numpy.random import seed
from numpy.random import randn
from statsmodels.graphics.gofplots import qqplot
# seed the random number generator
seed(1)
# generate univariate observations
data = 5 * randn(100) + 50
# q-q plot
qqplot(HCC1806_unf, line='s')
plt.show()

We compare the QQplot in the filtered and normalized case:

In [ ]:
# QQ Plot
from numpy.random import seed
from numpy.random import randn
from statsmodels.graphics.gofplots import qqplot
# seed the random number generator
seed(1)
# generate univariate observations
data = 5 * randn(100) + 50
# q-q plot
qqplot(HCC1806_f_n, line='s')
plt.show()

In reality, it's very unlikely to find data that are normally distributed. Also in this case, as we can see by plotting the QQ-plot, the data are not normally distributed, in fact, the data points in the plot are not close to the red line.

Log_2

We can now try to compute the log_2 of all the dataset, after adding 1 to it (do don't have problems with the zeros), and see if it can be a good normalization by looking again to the plot of the skenwness and the curtosis.

In [ ]:
HCC1806_unf_plus = HCC1806_unf + 1
HCC1806_unf_log2 = HCC1806_unf_plus.apply(np.log2)
HCC1806_unf_log2.describe()
Out[ ]:
"output.STAR.PCRPlate1A10_Normoxia_S123_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A12_Normoxia_S26_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A1_Hypoxia_S97_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A2_Hypoxia_S104_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A3_Hypoxia_S4_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A4_Hypoxia_S8_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A5_Hypoxia_S108_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A6_Hypoxia_S11_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A7_Normoxia_S113_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1A8_Normoxia_S119_Aligned.sortedByCoord.out.bam" ... "output.STAR.PCRPlate4G12_Normoxia_S243_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G1_Hypoxia_S193_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G2_Hypoxia_S198_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G6_Hypoxia_S232_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G7_Normoxia_S204_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H10_Normoxia_S210_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H11_Normoxia_S214_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H2_Hypoxia_S199_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H7_Normoxia_S205_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H9_Normoxia_S236_Aligned.sortedByCoord.out.bam"
count 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 ... 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000 23396.000000
mean 2.665234 3.224613 1.366411 2.261582 2.109583 1.827055 2.635027 2.887775 2.028888 1.877170 ... 2.822969 2.797182 2.234019 2.030740 2.048194 3.118012 2.252949 2.805019 2.163035 2.764438
std 3.341225 3.853466 1.938462 3.620534 2.760889 2.810320 3.651689 3.546553 2.807174 2.831652 ... 3.245582 3.438419 2.969904 2.611961 2.648009 3.413622 2.758163 3.443798 2.781778 3.167457
min 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
25% 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
50% 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... 1.000000 0.000000 0.000000 0.000000 0.000000 1.584963 0.000000 0.000000 0.000000 1.000000
75% 5.700440 6.977280 2.584963 5.357552 4.523562 4.169925 6.357552 6.266787 4.523562 4.247928 ... 5.832890 6.087463 4.906891 4.247928 4.321928 6.266787 4.643856 6.108524 4.523562 5.491853
max 15.114637 16.075751 12.632995 16.099327 14.080734 15.533908 15.394798 15.938799 14.884218 15.113539 ... 14.260773 14.919422 14.418314 13.716176 13.487966 15.030279 13.911017 15.073430 13.414949 14.800344

8 rows × 243 columns

Histogram of the mean

In [ ]:
# To plot an histogram with the means
sns.displot(data = HCC1806_unf_log2.describe().iloc[1], bins=50, color="teal")
plt.show()

Histogram of the third quantile

In [ ]:
# To plot an histogram with the third quantile
sns.displot(data = HCC1806_unf_log2.describe().iloc[6], bins=50, color="teal")
plt.show()

We can see that we still have some zeroes, but way less than before. We have also a much smaller range of values.

Let's now plot again the skeness and the curtosis of the cells, but of the dataset where we pwerformed the logarithms.

In [ ]:
cnames = HCC1806_unf_log2.columns
In [ ]:
# To calculate the skewness
from scipy.stats import kurtosis, skew

colN = np.shape(HCC1806_unf_log2)[1]
colN
df_skew_cells = []
for i in range(colN) :     
     v_df = HCC1806_unf_log2[cnames[i]]
     df_skew_cells += [skew(v_df)]   
  #  df_skew_cells += [df[cnames[i]].skew()]
df_skew_cells

plt.figure(figsize=(10,7))
sns.histplot(df_skew_cells, bins=100, color="teal")
plt.xlabel('Skewness of single cells expression profiles - log_2 df')
plt.show()
In [ ]:
# To calculate the kurtosis
df_kurt_cells = []
for i in range(colN) :     
     v_df = HCC1806_unf_log2[cnames[i]]
     df_kurt_cells += [kurtosis(v_df)]   
 #   df_kurt_cells += [df[cnames[i]].kurt()]
df_kurt_cells

plt.figure(figsize=(10,7))
sns.histplot(df_kurt_cells, bins=100, color="teal")
plt.xlabel('Kurtosis of single cells expression profiles - log_2 df')
plt.show()

We can definetely see that the data is much more normalized because most of the skewnwss and curtosis (not of all cells but most) is equal to 0. With respect to the MCF7 unfiltered dataset, the skewness of the new data is less near 0.

Filtered data

MCF7

Understanding the data

We now proceed by analysing the filtered and normalized data, in particular we look at the correlation between genes, differences between hypoxic and normoxic cells, their clustering and their skewness.

In [ ]:
MCF7_f_n.head()
Out[ ]:
"output.STAR.2_B3_Norm_S57_Aligned.sortedByCoord.out.bam" "output.STAR.2_B4_Norm_S58_Aligned.sortedByCoord.out.bam" "output.STAR.2_B5_Norm_S59_Aligned.sortedByCoord.out.bam" "output.STAR.2_B6_Norm_S60_Aligned.sortedByCoord.out.bam" "output.STAR.2_B7_Hypo_S79_Aligned.sortedByCoord.out.bam" "output.STAR.2_B9_Hypo_S81_Aligned.sortedByCoord.out.bam" "output.STAR.2_C10_Hypo_S130_Aligned.sortedByCoord.out.bam" "output.STAR.2_C11_Hypo_S131_Aligned.sortedByCoord.out.bam" "output.STAR.2_C1_Norm_S103_Aligned.sortedByCoord.out.bam" "output.STAR.2_C2_Norm_S104_Aligned.sortedByCoord.out.bam" ... "output.STAR.4_H10_Hypo_S382_Aligned.sortedByCoord.out.bam" "output.STAR.4_H14_Hypo_S383_Aligned.sortedByCoord.out.bam" "output.STAR.4_H1_Norm_S355_Aligned.sortedByCoord.out.bam" "output.STAR.4_H3_Norm_S357_Aligned.sortedByCoord.out.bam" "output.STAR.4_H4_Norm_S358_Aligned.sortedByCoord.out.bam" "output.STAR.4_H5_Norm_S359_Aligned.sortedByCoord.out.bam" "output.STAR.4_H6_Norm_S360_Aligned.sortedByCoord.out.bam" "output.STAR.4_H7_Hypo_S379_Aligned.sortedByCoord.out.bam" "output.STAR.4_H8_Hypo_S380_Aligned.sortedByCoord.out.bam" "output.STAR.4_H9_Hypo_S381_Aligned.sortedByCoord.out.bam"
"CYP1B1" 343 131 452 27 5817 3841 9263 21543 1013 53 ... 7890 4512 160 351 327 196 504 34565 20024 5953
"CYP1B1-AS1" 140 59 203 7 2669 1565 3866 9113 459 22 ... 3647 2035 75 138 130 102 238 13717 7835 2367
"CYP1A1" 0 0 0 0 0 79 238 443 0 0 ... 86 1654 0 0 0 1 0 11274 563 522
"NDRG1" 0 1 0 0 654 1263 2634 540 0 13 ... 481 1052 0 0 54 243 62 1263 925 1572
"DDIT4" 386 289 0 288 2484 2596 1323 2044 36 204 ... 3692 2410 800 1 189 266 417 4256 12733 2275

5 rows × 250 columns

In [ ]:
MCF7_f_n_describe = MCF7_f_n.T.describe()
MCF7_f_n_describe
Out[ ]:
"CYP1B1" "CYP1B1-AS1" "CYP1A1" "NDRG1" "DDIT4" "PFKFB3" "HK2" "AREG" "MYBL2" "ADM" ... "CD27-AS1" "DNAI7" "MAFG" "LZTR1" "BCO2" "GRIK5" "SLC25A27" "DENND5A" "CDK5R1" "FAM13A-AS1"
count 250.000000 250.000000 250.000000 250.000000 250.000000 250.000000 250.000000 250.000000 250.000000 250.000000 ... 250.000000 250.000000 250.000000 250.000000 250.000000 250.000000 250.000000 250.000000 250.000000 250.000000
mean 5454.536000 2258.572000 1604.580000 606.380000 2487.000000 1495.920000 868.424000 308.984000 394.988000 183.096000 ... 22.036000 0.192000 50.884000 23.308000 0.192000 0.256000 0.160000 60.536000 2.860000 5.952000
std 8282.337795 3453.650882 5657.397449 766.718881 3422.213185 2109.376474 1837.399974 592.950034 564.259514 470.374582 ... 43.250493 2.000787 69.729761 36.415015 1.309195 2.001622 1.167842 75.647093 8.839056 21.649028
min 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
25% 200.750000 85.000000 0.000000 1.000000 96.000000 71.000000 8.250000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 13.250000 0.000000 0.000000 0.000000 0.000000 11.250000 0.000000 0.000000
50% 795.000000 321.500000 0.000000 222.500000 1198.500000 369.500000 139.500000 18.000000 123.500000 0.000000 ... 8.000000 0.000000 37.000000 1.000000 0.000000 0.000000 0.000000 38.500000 0.000000 0.000000
75% 8180.500000 3348.500000 284.500000 1077.500000 3720.000000 2180.750000 1008.000000 371.000000 629.000000 74.500000 ... 30.000000 0.000000 63.000000 41.000000 0.000000 0.000000 0.000000 77.000000 0.000000 0.000000
max 44406.000000 17673.000000 58717.000000 3884.000000 21994.000000 12078.000000 16625.000000 3496.000000 3108.000000 3586.000000 ... 509.000000 28.000000 816.000000 196.000000 14.000000 26.000000 11.000000 639.000000 62.000000 288.000000

8 rows × 3000 columns

We look at the statistical data about the transposed data to compare differences in expression among genes. There are still many cells where mean is equal to 0 and many cells where the 75% quantile is equal to 0.

In [ ]:
sns.displot(data = MCF7_f_n_describe.iloc[1], bins=500, color="teal")
plt.xlim(-10, 2500)
plt.show()
In [ ]:
sns.displot(data = MCF7_f_n_describe.iloc[6], bins=500, color="teal")
plt.xlim(-10, 2500)
plt.show()
Correlation
In [ ]:
# To see the correlation between genes
df_new = MCF7_f_n.transpose().iloc[:,:25]
plt.figure(figsize=(25,25))
sns.heatmap(df_new.corr(),cbar=True,annot=True,cmap='Blues')
plt.show()
Hypo vs Norm

It can be quite interesting to see if there are major differences between the gene expressions in cells under hypoxic or normoxic conditions.

In [ ]:
# Hypoxic cells using filtered and normalized dataset
MCF7_Hypo_f_n = MCF7_f_n.loc[:, MCF7_f_n.columns.str.contains('Hypo')]
MCF7_Hypo_f_n
Out[ ]:
"output.STAR.2_B7_Hypo_S79_Aligned.sortedByCoord.out.bam" "output.STAR.2_B9_Hypo_S81_Aligned.sortedByCoord.out.bam" "output.STAR.2_C10_Hypo_S130_Aligned.sortedByCoord.out.bam" "output.STAR.2_C11_Hypo_S131_Aligned.sortedByCoord.out.bam" "output.STAR.2_C8_Hypo_S128_Aligned.sortedByCoord.out.bam" "output.STAR.2_C9_Hypo_S129_Aligned.sortedByCoord.out.bam" "output.STAR.2_D10_Hypo_S178_Aligned.sortedByCoord.out.bam" "output.STAR.2_D11_Hypo_S179_Aligned.sortedByCoord.out.bam" "output.STAR.2_D12_Hypo_S180_Aligned.sortedByCoord.out.bam" "output.STAR.2_D7_Hypo_S175_Aligned.sortedByCoord.out.bam" ... "output.STAR.4_G11_Hypo_S335_Aligned.sortedByCoord.out.bam" "output.STAR.4_G12_Hypo_S336_Aligned.sortedByCoord.out.bam" "output.STAR.4_G7_Hypo_S331_Aligned.sortedByCoord.out.bam" "output.STAR.4_G8_Hypo_S332_Aligned.sortedByCoord.out.bam" "output.STAR.4_G9_Hypo_S333_Aligned.sortedByCoord.out.bam" "output.STAR.4_H10_Hypo_S382_Aligned.sortedByCoord.out.bam" "output.STAR.4_H14_Hypo_S383_Aligned.sortedByCoord.out.bam" "output.STAR.4_H7_Hypo_S379_Aligned.sortedByCoord.out.bam" "output.STAR.4_H8_Hypo_S380_Aligned.sortedByCoord.out.bam" "output.STAR.4_H9_Hypo_S381_Aligned.sortedByCoord.out.bam"
"CYP1B1" 5817 3841 9263 21543 1338 10043 3435 8579 3111 12164 ... 13805 27531 10805 2165 17970 7890 4512 34565 20024 5953
"CYP1B1-AS1" 2669 1565 3866 9113 554 4191 1624 3974 1374 5871 ... 5937 11426 4712 941 7653 3647 2035 13717 7835 2367
"CYP1A1" 0 79 238 443 14 50 170 4312 0 1 ... 2658 58717 1844 4171 1 86 1654 11274 563 522
"NDRG1" 654 1263 2634 540 634 1084 460 1292 1339 869 ... 943 925 1206 488 781 481 1052 1263 925 1572
"DDIT4" 2484 2596 1323 2044 3513 2438 1668 4602 2456 10157 ... 3768 4921 4712 4196 4098 3692 2410 4256 12733 2275
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
"GRIK5" 0 0 0 0 0 6 0 0 0 0 ... 2 0 0 0 0 0 0 0 0 0
"SLC25A27" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"DENND5A" 60 107 74 127 14 0 18 31 0 18 ... 78 15 54 0 219 179 97 140 7 37
"CDK5R1" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"FAM13A-AS1" 0 0 0 13 0 0 20 0 14 0 ... 0 0 3 53 0 0 0 32 11 12

3000 rows × 124 columns

In [ ]:
# To transpose the hypoxic dataset
MCF7_Hypo_f_n_trans = MCF7_Hypo_f_n.transpose()
MCF7_Hypo_f_n_trans
Out[ ]:
"CYP1B1" "CYP1B1-AS1" "CYP1A1" "NDRG1" "DDIT4" "PFKFB3" "HK2" "AREG" "MYBL2" "ADM" ... "CD27-AS1" "DNAI7" "MAFG" "LZTR1" "BCO2" "GRIK5" "SLC25A27" "DENND5A" "CDK5R1" "FAM13A-AS1"
"output.STAR.2_B7_Hypo_S79_Aligned.sortedByCoord.out.bam" 5817 2669 0 654 2484 1603 748 436 0 0 ... 0 0 63 0 0 0 0 60 0 0
"output.STAR.2_B9_Hypo_S81_Aligned.sortedByCoord.out.bam" 3841 1565 79 1263 2596 2795 3970 373 554 31 ... 0 0 102 42 0 0 0 107 0 0
"output.STAR.2_C10_Hypo_S130_Aligned.sortedByCoord.out.bam" 9263 3866 238 2634 1323 2624 1265 646 0 0 ... 0 0 92 0 0 0 0 74 0 0
"output.STAR.2_C11_Hypo_S131_Aligned.sortedByCoord.out.bam" 21543 9113 443 540 2044 3449 2034 0 0 2170 ... 4 0 120 56 0 0 0 127 0 13
"output.STAR.2_C8_Hypo_S128_Aligned.sortedByCoord.out.bam" 1338 554 14 634 3513 1360 303 558 178 994 ... 0 0 46 5 0 0 0 14 0 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
"output.STAR.4_H10_Hypo_S382_Aligned.sortedByCoord.out.bam" 7890 3647 86 481 3692 4702 1011 2707 144 385 ... 0 0 0 20 0 0 0 179 0 0
"output.STAR.4_H14_Hypo_S383_Aligned.sortedByCoord.out.bam" 4512 2035 1654 1052 2410 2561 999 717 175 612 ... 0 0 62 22 0 0 0 97 0 0
"output.STAR.4_H7_Hypo_S379_Aligned.sortedByCoord.out.bam" 34565 13717 11274 1263 4256 5663 701 0 0 0 ... 0 0 45 0 0 0 0 140 0 32
"output.STAR.4_H8_Hypo_S380_Aligned.sortedByCoord.out.bam" 20024 7835 563 925 12733 2187 1141 0 20 81 ... 0 0 57 8 0 0 0 7 0 11
"output.STAR.4_H9_Hypo_S381_Aligned.sortedByCoord.out.bam" 5953 2367 522 1572 2275 3269 2247 169 2 0 ... 0 0 165 0 0 0 0 37 0 12

124 rows × 3000 columns

In [ ]:
# To check the characteristics of the genes in the hypoxic cells
MCF7_Hypo_f_n_trans_d = MCF7_Hypo_f_n_trans.describe()
MCF7_Hypo_f_n_trans_d
Out[ ]:
"CYP1B1" "CYP1B1-AS1" "CYP1A1" "NDRG1" "DDIT4" "PFKFB3" "HK2" "AREG" "MYBL2" "ADM" ... "CD27-AS1" "DNAI7" "MAFG" "LZTR1" "BCO2" "GRIK5" "SLC25A27" "DENND5A" "CDK5R1" "FAM13A-AS1"
count 124.000000 124.000000 124.000000 124.000000 124.000000 124.000000 124.000000 124.000000 124.000000 124.000000 ... 124.000000 124.000000 124.000000 124.000000 124.000000 124.000000 124.000000 124.000000 124.000000 124.000000
mean 10696.193548 4430.491935 3233.911290 1203.637097 4663.588710 2855.653226 1721.572581 508.903226 137.572581 367.370968 ... 17.491935 0.274194 74.709677 17.677419 0.306452 0.483871 0.250000 91.443548 1.491935 11.604839
std 9155.215917 3833.386820 7712.505628 688.882910 3720.342842 2285.651842 2318.531078 755.171271 408.994050 616.390324 ... 53.238457 2.551386 89.603442 35.021143 1.753869 2.806739 1.446189 93.872453 7.831037 29.652957
min 7.000000 1.000000 0.000000 149.000000 46.000000 47.000000 40.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
25% 3798.000000 1590.500000 0.000000 665.250000 2452.500000 1262.750000 553.750000 0.000000 0.000000 8.250000 ... 0.000000 0.000000 29.750000 0.000000 0.000000 0.000000 0.000000 30.000000 0.000000 0.000000
50% 8394.500000 3357.500000 307.000000 1092.500000 3747.000000 2208.000000 1019.500000 86.000000 0.500000 78.000000 ... 0.000000 0.000000 54.500000 0.000000 0.000000 0.000000 0.000000 69.500000 0.000000 0.000000
75% 15049.000000 6254.500000 2554.500000 1573.000000 5397.000000 4285.250000 1998.000000 854.000000 95.000000 411.500000 ... 19.250000 0.000000 94.000000 24.500000 0.000000 0.000000 0.000000 119.500000 0.000000 16.000000
max 44406.000000 17673.000000 58717.000000 3884.000000 21994.000000 12078.000000 16625.000000 3496.000000 2647.000000 3586.000000 ... 509.000000 28.000000 816.000000 189.000000 14.000000 26.000000 11.000000 639.000000 62.000000 288.000000

8 rows × 3000 columns

We considered only the hypoxic cells and transposed the dataset to analyse the expression of the genes, in particular we immediately saw that some genes are expressed in mean with a value close to 0 and others are over 10,000, hence some genes seem more relevant to hypoxic cells.

We did the same procedure with the normoxic cells and saw that also in this case some genes are much more expressed than others.

In [ ]:
# Normoxic cells using filtered and transposed data
MCF7_Norm_f_n = MCF7_f_n.loc[:, MCF7_f_n.columns.str.contains('Norm')]
MCF7_Norm_f_n
Out[ ]:
"output.STAR.2_B3_Norm_S57_Aligned.sortedByCoord.out.bam" "output.STAR.2_B4_Norm_S58_Aligned.sortedByCoord.out.bam" "output.STAR.2_B5_Norm_S59_Aligned.sortedByCoord.out.bam" "output.STAR.2_B6_Norm_S60_Aligned.sortedByCoord.out.bam" "output.STAR.2_C1_Norm_S103_Aligned.sortedByCoord.out.bam" "output.STAR.2_C2_Norm_S104_Aligned.sortedByCoord.out.bam" "output.STAR.2_C3_Norm_S105_Aligned.sortedByCoord.out.bam" "output.STAR.2_C4_Norm_S106_Aligned.sortedByCoord.out.bam" "output.STAR.2_C5_Norm_S107_Aligned.sortedByCoord.out.bam" "output.STAR.2_C6_Norm_S108_Aligned.sortedByCoord.out.bam" ... "output.STAR.4_G2_Norm_S308_Aligned.sortedByCoord.out.bam" "output.STAR.4_G3_Norm_S309_Aligned.sortedByCoord.out.bam" "output.STAR.4_G4_Norm_S310_Aligned.sortedByCoord.out.bam" "output.STAR.4_G5_Norm_S311_Aligned.sortedByCoord.out.bam" "output.STAR.4_G6_Norm_S312_Aligned.sortedByCoord.out.bam" "output.STAR.4_H1_Norm_S355_Aligned.sortedByCoord.out.bam" "output.STAR.4_H3_Norm_S357_Aligned.sortedByCoord.out.bam" "output.STAR.4_H4_Norm_S358_Aligned.sortedByCoord.out.bam" "output.STAR.4_H5_Norm_S359_Aligned.sortedByCoord.out.bam" "output.STAR.4_H6_Norm_S360_Aligned.sortedByCoord.out.bam"
"CYP1B1" 343 131 452 27 1013 53 237 239 118 58 ... 801 0 923 485 1 160 351 327 196 504
"CYP1B1-AS1" 140 59 203 7 459 22 98 99 54 19 ... 294 0 441 192 0 75 138 130 102 238
"CYP1A1" 0 0 0 0 0 0 1 0 0 0 ... 0 0 0 0 0 0 0 0 1 0
"NDRG1" 0 1 0 0 0 13 0 0 10 0 ... 0 0 52 63 131 0 0 54 243 62
"DDIT4" 386 289 0 288 36 204 167 17 315 349 ... 91 294 125 45 1501 800 1 189 266 417
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
"GRIK5" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"SLC25A27" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"DENND5A" 51 34 0 4 0 66 1 77 17 90 ... 0 7 6 0 62 0 35 56 45 0
"CDK5R1" 0 0 0 0 0 8 0 0 0 0 ... 0 0 0 18 0 26 0 0 19 0
"FAM13A-AS1" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0

3000 rows × 126 columns

In [ ]:
# To transpose the normoxic dataset
MCF7_Norm_f_n_trans = MCF7_Norm_f_n.transpose()
MCF7_Norm_f_n_trans
Out[ ]:
"CYP1B1" "CYP1B1-AS1" "CYP1A1" "NDRG1" "DDIT4" "PFKFB3" "HK2" "AREG" "MYBL2" "ADM" ... "CD27-AS1" "DNAI7" "MAFG" "LZTR1" "BCO2" "GRIK5" "SLC25A27" "DENND5A" "CDK5R1" "FAM13A-AS1"
"output.STAR.2_B3_Norm_S57_Aligned.sortedByCoord.out.bam" 343 140 0 0 386 75 0 0 476 0 ... 63 0 17 59 0 0 0 51 0 0
"output.STAR.2_B4_Norm_S58_Aligned.sortedByCoord.out.bam" 131 59 0 1 289 42 0 856 1586 0 ... 0 0 1 25 0 0 0 34 0 0
"output.STAR.2_B5_Norm_S59_Aligned.sortedByCoord.out.bam" 452 203 0 0 0 0 0 0 775 0 ... 15 0 23 0 0 0 0 0 0 0
"output.STAR.2_B6_Norm_S60_Aligned.sortedByCoord.out.bam" 27 7 0 0 288 214 15 242 1191 0 ... 1 0 3 10 0 0 0 4 0 0
"output.STAR.2_C1_Norm_S103_Aligned.sortedByCoord.out.bam" 1013 459 0 0 36 75 15 6 1120 0 ... 0 0 80 0 0 0 0 0 0 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
"output.STAR.4_H1_Norm_S355_Aligned.sortedByCoord.out.bam" 160 75 0 0 800 1041 39 0 0 0 ... 35 0 0 35 0 0 0 0 26 0
"output.STAR.4_H3_Norm_S357_Aligned.sortedByCoord.out.bam" 351 138 0 0 1 57 26 0 331 0 ... 10 0 12 2 0 0 0 35 0 0
"output.STAR.4_H4_Norm_S358_Aligned.sortedByCoord.out.bam" 327 130 0 54 189 235 232 1 1 0 ... 13 0 26 0 0 0 0 56 0 0
"output.STAR.4_H5_Norm_S359_Aligned.sortedByCoord.out.bam" 196 102 1 243 266 278 78 1 199 0 ... 79 0 1 0 0 0 0 45 19 0
"output.STAR.4_H6_Norm_S360_Aligned.sortedByCoord.out.bam" 504 238 0 62 417 932 275 0 33 0 ... 86 0 0 0 0 0 0 0 0 0

126 rows × 3000 columns

In [ ]:
# To check the characteristics of the genes in normoxic cells
MCF7_Norm_f_n_trans_d = MCF7_Norm_f_n_trans.describe()
MCF7_Norm_f_n_trans_d
Out[ ]:
"CYP1B1" "CYP1B1-AS1" "CYP1A1" "NDRG1" "DDIT4" "PFKFB3" "HK2" "AREG" "MYBL2" "ADM" ... "CD27-AS1" "DNAI7" "MAFG" "LZTR1" "BCO2" "GRIK5" "SLC25A27" "DENND5A" "CDK5R1" "FAM13A-AS1"
count 126.000000 126.000000 126.000000 126.000000 126.000000 126.000000 126.000000 126.000000 126.000000 126.000000 ... 126.000000 126.000000 126.000000 126.000000 126.000000 126.000000 126.000000 126.000000 126.000000 126.000000
mean 296.079365 121.126984 1.111111 18.603175 344.960317 157.769841 28.817460 112.238095 648.317460 1.746032 ... 26.507937 0.111111 27.436508 28.849206 0.079365 0.031746 0.071429 30.119048 4.206349 0.388889
std 301.404382 124.625325 7.706851 44.026734 620.660453 289.259279 53.607671 246.050968 582.416478 6.318147 ... 29.943613 1.247219 25.844921 37.043772 0.601374 0.356348 0.801784 29.118958 9.571054 2.342553
min 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
25% 36.500000 14.000000 0.000000 0.000000 22.000000 24.250000 0.000000 0.000000 144.000000 0.000000 ... 1.000000 0.000000 4.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000
50% 228.000000 99.000000 0.000000 1.000000 97.000000 71.000000 8.500000 2.000000 555.000000 0.000000 ... 18.500000 0.000000 22.500000 15.000000 0.000000 0.000000 0.000000 23.500000 0.000000 0.000000
75% 422.250000 175.000000 0.000000 16.250000 317.250000 156.500000 34.500000 73.750000 966.750000 0.000000 ... 39.000000 0.000000 41.750000 45.250000 0.000000 0.000000 0.000000 51.000000 0.000000 0.000000
max 1522.000000 596.000000 78.000000 296.000000 3506.000000 2111.000000 284.000000 1673.000000 3108.000000 41.000000 ... 165.000000 14.000000 125.000000 196.000000 6.000000 4.000000 9.000000 115.000000 55.000000 18.000000

8 rows × 3000 columns

In [ ]:
df_small = MCF7_Hypo_f_n.transpose().iloc[:, :50]
plt.figure(figsize=(16,4))
plot=sns.violinplot(data=df_small,palette="Set3",cut=0)
plt.setp(plot.get_xticklabels(), rotation=90)
plt.show()
In [ ]:
df_small = MCF7_Norm_f_n.transpose().iloc[:, :50]
plt.figure(figsize=(16,4))
plot=sns.violinplot(data=df_small,palette="Set3",cut=0)
plt.setp(plot.get_xticklabels(), rotation=90)
plt.show()

From the filtered and normalized violin plots it emerges that some genes are much more expressed in hypoxic cells than in normoxic cells (and viceversa). It is difficult to see from just the first 50 genes in the violin plots, later we will analyze the difference between some specific genes.\ We can see, for example, that the mean and the 25% and 75% quantile for the CYP1B1 gene are very different between the hypoxic and normoxic cells.

Let's now look for the genes that appear, either in diff or ratio of the means, to be more important in the differentiation between hypoxic and normoxic cells.

In [ ]:
# To calculate the difference in mean for each gene in hypoxic and normoxic cells
MCF7_f_n_meandiff = MCF7_Hypo_f_n_trans_d.iloc[1] - MCF7_Norm_f_n_trans_d.iloc[1]
MCF7_f_n_meandiff
Out[ ]:
"CYP1B1"        10400.114183
"CYP1B1-AS1"     4309.364951
"CYP1A1"         3232.800179
"NDRG1"          1185.033922
"DDIT4"          4318.628392
                    ...     
"GRIK5"             0.452125
"SLC25A27"          0.178571
"DENND5A"          61.324501
"CDK5R1"           -2.714414
"FAM13A-AS1"       11.215950
Name: mean, Length: 3000, dtype: float64
In [ ]:
# To sort the mean differences found
MCF7_f_n_meandiff_sorted = MCF7_f_n_meandiff.sort_values(ascending=False)
MCF7_f_n_meandiff_sorted
Out[ ]:
"GAPDH"     37668.952893
"ACTG1"     21697.537378
"ALDOA"     20955.116999
"CYP1B1"    10400.114183
"FTH1"       7711.505888
                ...     
"SULF2"     -1934.329109
"MT-CO3"    -2375.729903
"MT-CO2"    -3872.005376
"MT-CYB"    -4408.886585
"MT-CO1"    -6474.568868
Name: mean, Length: 3000, dtype: float64

We want to compare the gene expression across cells, so we find the difference between the gene expression in mean for hypoxic and normoxic cells and sort them. The first values show us the genes that are much more expressed in hypoxic cells than in normoxic cells, whereas the last values shows us the ones much more expressed in normoxic cells.

Using the ratio of means

In [ ]:
# To calculate the ratio between the means of each gene in hypoxic and normoxic cells
MCF7_f_n_meanratio = (MCF7_Hypo_f_n_trans_d.iloc[1])/(MCF7_Norm_f_n_trans_d.iloc[1])
MCF7_f_n_meanratio
Out[ ]:
"CYP1B1"          36.126103
"CYP1B1-AS1"      36.577250
"CYP1A1"        2910.520161
"NDRG1"           64.700629
"DDIT4"           13.519203
                   ...     
"GRIK5"           15.241935
"SLC25A27"         3.500000
"DENND5A"          3.036070
"CDK5R1"           0.354687
"FAM13A-AS1"      29.841014
Name: mean, Length: 3000, dtype: float64
In [ ]:
# To sort the ratios between the means found
MCF7_f_n_meanratio_sorted = MCF7_f_n_meanratio.sort_values(ascending=False)
MCF7_f_n_meanratio_sorted
Out[ ]:
"S1PR4"      inf
"IFIT2"      inf
"TRBV30"     inf
"ADGRF2"     inf
"CNTN3"      inf
            ... 
"RARRES2"    0.0
"ZDHHC22"    0.0
"NTRK3"      0.0
"ADGRG5"     0.0
"DMBX1"      0.0
Name: mean, Length: 3000, dtype: float64

To get a more accurate comparison we repeat the same procedure by calculating the ratio between the mean gene expression in hypoxic and normoxic cells. Since some genes have mean expression 0, as a result we obtain both infinite and 0 values. Since in this case the comparison between the ratios is significant only with non-zero terms, we exclude such genes and compare the remaining ones.

In [ ]:
# To remove the infinite values in the list
MCF7_f_n_meanratio_sorted.replace([np.inf, -np.inf], np.nan, inplace=True)
MCF7_f_n_meanratio_sorted.replace(0, np.nan, inplace=True)
MCF7_f_n_meanratio_sorted.dropna(inplace=True)
MCF7_f_n_meanratio_sorted
Out[ ]:
"CYP1A1"        2910.520161
"NPC1L1"        1014.096774
"DAPP1"          922.645161
"ENOX1"          564.967742
"MANCR"          332.274194
                   ...     
"CD22"             0.004361
"TRPC6"            0.004252
"INSYN1-AS1"       0.002957
"ACE"              0.002283
"KCNK5"            0.000911
Name: mean, Length: 2886, dtype: float64

Because this is extremely aprooximate and because many ratios where either 0 or infinite, we compute the ratio betwen the log_2 of the mean + 1 and we return the values sorted.

In [ ]:
MCF7_f_n_logratio = np.log2(MCF7_Hypo_f_n_trans_d.iloc[1] + 1) - np.log2(MCF7_Norm_f_n_trans_d.iloc[1] + 1)
MCF7_f_n_logratio.sort_values(ascending=False)
Out[ ]:
"CYP1A1"    10.581508
"ADM"        7.067667
"IGFBP3"     6.701573
"KRT17"      6.650212
"NDRG1"      5.941367
              ...    
"ELOVL2"    -4.336349
"IL27RA"    -4.484711
"SFXN2"     -4.502608
"MGP"       -4.628474
"RAMP1"     -4.919597
Name: mean, Length: 3000, dtype: float64
Check with random forest which cells have higher importance

We now try to get the most important genes with a random forest to check wheter they are the same as the ones we found before.

In [ ]:
data_test = MCF7_f_n
In [ ]:
# Let's load the packages
import numpy as np
import pandas as pd
from sklearn.datasets import load_boston
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestRegressor
from sklearn.inspection import permutation_importance
#import shap
from matplotlib import pyplot as plt

plt.rcParams.update({'figure.figsize': (12.0, 8.0)})
plt.rcParams.update({'font.size': 14})
In [ ]:
index = data_test.T.index
y = np.zeros((len(index)),dtype = 'int64')
for i in range(len(index)):
    y[i] = not 'Hypo' in index[i] # 0 Hypo 1 Norm
In [ ]:
X_train, X_test, y_train, y_test = train_test_split(data_test.T, y, test_size= 0.1, random_state= 42)
In [ ]:
rf = RandomForestRegressor(n_estimators=100)
rf.fit(X_train, y_train)
Out[ ]:
RandomForestRegressor()
In [ ]:
genes_importance = rf.feature_importances_
In [ ]:
genes = {}
for n, g in zip(data_test.index, genes_importance):
  genes[n] = g
print({k: v for k, v in sorted(genes.items(), key=lambda item: item[1], reverse=True)})
{'"NDRG1"': 0.6223078526879188, '"GAPDH"': 0.15508077494604888, '"MT-CO3"': 0.13425458853916902, '"MT-CYB"': 0.03893954522647767, '"BNIP3"': 0.019128316830396595, '"P4HA1"': 0.0017245829719825985, '"A4GALT"': 0.0010388211319290715, '"MUC5AC"': 0.0008801233011419186, '"HK2"': 0.0008727969961314983, '"FASN"': 0.0008695306377398602, '"PDK1"': 0.000863594487476328, '"MUC16"': 0.0007010437762891417, '"ERO1A"': 0.0006947660954145455, '"EBP"': 0.0006892507000509241, '"MVD"': 0.0006866036008544401, '"GRB10"': 0.0005285412262156453, '"HLA-C"': 0.0005269574991775217, '"PFKP"': 0.0005262114314840362, '"TXNRD1"': 0.0005226480836236949, '"SLC9A3R1"': 0.0005219610269099912, '"CD9"': 0.0005213562987564688, '"SLC25A39"': 0.0005208333333333347, '"KRT17"': 0.0005203916428956906, '"ESR1"': 0.0003599424092145257, '"MTATP6P1"': 0.0003568164109326319, '"EEF1GP4"': 0.0003535353535353536, '"IL27RA"': 0.00035294117647058837, '"RAMP3"': 0.00035233322893830254, '"ADGRE2"': 0.00035233322893830145, '"RHOD"': 0.0003517823639774857, '"TMSB10"': 0.00035123966942148633, '"SQLE"': 0.00035084983627007644, '"DCXR"': 0.00035046728971962647, '"DDX41"': 0.00035046728971962647, '"NECAB1"': 0.0003504672897196263, '"TM7SF2"': 0.0003504672897196257, '"CABLES1"': 0.00035014005602241124, '"ARMC9"': 0.00035014005602240886, '"TMEM64"': 0.0003498678277095329, '"TUBD1"': 0.0003498678277095321, '"EMP2"': 0.00034986782770953195, '"CYP1B1"': 0.00034965034965035106, '"LOXL1"': 0.0003496503496503497, '"IBA57-DT"': 0.0003496503496503497, '"MXD1"': 0.00034965034965034965, '"FOSL1"': 0.00034959792830857356, '"BNIP3L"': 0.0003494874184529363, '"CALCR"': 0.00034948741845293566, '"KRT13"': 0.00034937888198757766, '"GCK"': 0.00034937888198757766, '"SHH"': 0.00034932463903120635, '"TST"': 0.00034932463903120635, '"ADGRG5"': 0.00017936862244897957, '"PLAAT4"': 0.00017933009826030926, '"LPP"': 0.00017893217893218016, '"COTL1"': 0.00017857142857142803, '"SLC9A3R1-AS1"': 0.00017857142857142803, '"STC2"': 0.00017856000000000127, '"P2RY6"': 0.00017820000000000005, '"IBSP"': 0.00017789373814041754, '"ELOVL5"': 0.00017733291298865076, '"CHDH"': 0.00017709563164108622, '"IGSF1"': 0.00017709563164108462, '"MIR4435-2HG"': 0.00017709563164108462, '"RAB37"': 0.00017685439560439568, '"ERRFI1"': 0.00017670619649729147, '"ACAA2"': 0.00017669350573339454, '"TGIF1"': 0.00017655367231638556, '"MOV10"': 0.00017655367231638556, '"GADD45A"': 0.0001765536723163849, '"IER5"': 0.0001765536723163849, '"DSP"': 0.00017655367231638418, '"MUCL1"': 0.00017654077483137315, '"LARGE2"': 0.00017653825143488223, '"HNRNPMP1"': 0.00017642907551164436, '"TMEM109"': 0.0001764139495620991, '"OXER1"': 0.00017633228840125393, '"PPIF"': 0.00017633228840125393, '"PTPRN"': 0.00017633228840125366, '"INSYN1"': 0.00017626321974148064, '"CYP1B1-AS1"': 0.00017626321974148062, '"SAMD4A"': 0.00017626321974148032, '"DMPK"': 0.00017624965685907517, '"SMTNL2"': 0.0001762496568590746, '"GGN"': 0.0001762338180367698, '"LAMB3"': 0.00017622180451127827, '"INSYN1-AS1"': 0.00017622180451127824, '"KIF22"': 0.000176221804511278, '"LAMB2"': 0.0001762080037591038, '"GHDC"': 0.00017620750195430145, '"TNFAIP3"': 0.00017620750195430112, '"CYP1A1"': 0.0, '"DDIT4"': 0.0, '"PFKFB3"': 0.0, '"AREG"': 0.0, '"MYBL2"': 0.0, '"ADM"': 0.0, '"CDC20"': 0.0, '"KRT80"': 0.0, '"PLK1"': 0.0, '"TK1"': 0.0, '"GDF15"': 0.0, '"TFF1"': 0.0, '"KIF20A"': 0.0, '"VEGFA"': 0.0, '"BCAS1"': 0.0, '"RASD1"': 0.0, '"NR4A1"': 0.0, '"IGFBP3"': 0.0, '"SLC2A1"': 0.0, '"ITGA5"': 0.0, '"CCNB1"': 0.0, '"UBE2C"': 0.0, '"FOS"': 0.0, '"PFKFB4"': 0.0, '"CEACAM5"': 0.0, '"TGFBI"': 0.0, '"BHLHE40"': 0.0, '"LOXL2"': 0.0, '"LMCD1"': 0.0, '"BAMBI"': 0.0, '"RRM2"': 0.0, '"TUBA1B"': 0.0, '"TPX2"': 0.0, '"PRC1"': 0.0, '"CDKN1A"': 0.0, '"KPNA2"': 0.0, '"SPAG5"': 0.0, '"SPOCK1"': 0.0, '"AURKB"': 0.0, '"ANGPTL4"': 0.0, '"UGDH"': 0.0, '"ASF1B"': 0.0, '"HSPA6"': 0.0, '"FAM83D"': 0.0, '"IGFBP5"': 0.0, '"AURKA"': 0.0, '"HSPB8"': 0.0, '"PTTG1"': 0.0, '"GPRC5A"': 0.0, '"ZWINT"': 0.0, '"TIMP3"': 0.0, '"HILPDA"': 0.0, '"HMOX1"': 0.0, '"RGS16"': 0.0, '"DUSP4"': 0.0, '"PCDH10"': 0.0, '"DUSP1"': 0.0, '"DKK1"': 0.0, '"GFRA1"': 0.0, '"KIF2C"': 0.0, '"SLC7A5"': 0.0, '"PADI2"': 0.0, '"JAG1"': 0.0, '"ACKR3"': 0.0, '"TFF3"': 0.0, '"ELAPOR1"': 0.0, '"ST3GAL1"': 0.0, '"GSN"': 0.0, '"BMP7"': 0.0, '"TOP2A"': 0.0, '"UHRF1"': 0.0, '"ENO2"': 0.0, '"ANXA1"': 0.0, '"TRIB3"': 0.0, '"CCNB2"': 0.0, '"LRP4"': 0.0, '"CEACAM6"': 0.0, '"LINC00052"': 0.0, '"PREX1"': 0.0, '"GPER1"': 0.0, '"MCM7"': 0.0, '"PHLDA1"': 0.0, '"RAMP1"': 0.0, '"EDN2"': 0.0, '"DDIT3"': 0.0, '"KDM3A"': 0.0, '"CCN2"': 0.0, '"CCN5"': 0.0, '"SRF"': 0.0, '"CA9"': 0.0, '"MDK"': 0.0, '"MCM2"': 0.0, '"FEN1"': 0.0, '"TROAP"': 0.0, '"PIMREG"': 0.0, '"ARL6IP1"': 0.0, '"NUPR1"': 0.0, '"GSTM3"': 0.0, '"MCM5"': 0.0, '"NEDD9"': 0.0, '"TUBA4A"': 0.0, '"EPAS1"': 0.0, '"NTN4"': 0.0, '"SOX4"': 0.0, '"TRIM29"': 0.0, '"S100P"': 0.0, '"MKI67"': 0.0, '"IFI30"': 0.0, '"PTGER4"': 0.0, '"TRIM16"': 0.0, '"PHLDA1-AS1"': 0.0, '"KRT81"': 0.0, '"NR3C1"': 0.0, '"CASP14"': 0.0, '"EDN1"': 0.0, '"MCM3"': 0.0, '"CDC45"': 0.0, '"NR4A2"': 0.0, '"OVOL1"': 0.0, '"RECQL4"': 0.0, '"SCUBE2"': 0.0, '"E2F1"': 0.0, '"SERPINA3"': 0.0, '"SFXN2"': 0.0, '"XBP1"': 0.0, '"DHRS3"': 0.0, '"HJURP"': 0.0, '"GINS2"': 0.0, '"ALCAM"': 0.0, '"FOXO1"': 0.0, '"PKMYT1"': 0.0, '"AMIGO2"': 0.0, '"NUSAP1"': 0.0, '"TACC3"': 0.0, '"CCNF"': 0.0, '"PIF1"': 0.0, '"ITPRID2"': 0.0, '"INHA"': 0.0, '"IFFO2"': 0.0, '"ID1"': 0.0, '"CRABP2"': 0.0, '"CA2"': 0.0, '"UBC"': 0.0, '"ZYX"': 0.0, '"ELF3"': 0.0, '"HSPA1A"': 0.0, '"NCAPD2"': 0.0, '"TSC22D2"': 0.0, '"GPI"': 0.0, '"TUBB4B"': 0.0, '"MGP"': 0.0, '"SLC6A14"': 0.0, '"HMGB2"': 0.0, '"TNFRSF21"': 0.0, '"SQSTM1"': 0.0, '"PCP4"': 0.0, '"N4BP3"': 0.0, '"CIART"': 0.0, '"LGALS3BP"': 0.0, '"H4C3"': 0.0, '"MUC5B"': 0.0, '"KCNE4"': 0.0, '"MT-CO2"': 0.0, '"SIPA1L2"': 0.0, '"PKP3"': 0.0, '"PMEPA1"': 0.0, '"CALML5"': 0.0, '"EGLN3"': 0.0, '"RACGAP1"': 0.0, '"DSCAM-AS1"': 0.0, '"TUFT1"': 0.0, '"IQGAP3"': 0.0, '"CDCA3"': 0.0, '"CTSD"': 0.0, '"PPP1R3C"': 0.0, '"DUSP2"': 0.0, '"GRM4"': 0.0, '"SYBU"': 0.0, '"PIM1"': 0.0, '"MAOB"': 0.0, '"CAV1"': 0.0, '"ANLN"': 0.0, '"SAT1"': 0.0, '"KRT16"': 0.0, '"ID4"': 0.0, '"JUN"': 0.0, '"RAB31"': 0.0, '"ALDH1A3"': 0.0, '"STRA6"': 0.0, '"RBCK1"': 0.0, '"NAPRT"': 0.0, '"FHL2"': 0.0, '"SLC39A6"': 0.0, '"MCM10"': 0.0, '"SLC25A25"': 0.0, '"SLC12A4"': 0.0, '"CDCA5"': 0.0, '"ESPL1"': 0.0, '"NPC1L1"': 0.0, '"EGR2"': 0.0, '"CCNA2"': 0.0, '"HEY1"': 0.0, '"CDCA8"': 0.0, '"ANXA9"': 0.0, '"SEMA5B"': 0.0, '"NR4A1AS"': 0.0, '"PGK1"': 0.0, '"DLC1"': 0.0, '"RGCC"': 0.0, '"GOLM1"': 0.0, '"LDHA"': 0.0, '"BUB1"': 0.0, '"ACTG2"': 0.0, '"KLF6"': 0.0, '"WNT11"': 0.0, '"PLIN2"': 0.0, '"STARD10"': 0.0, '"PHGDH"': 0.0, '"SPTSSB"': 0.0, '"JUNB"': 0.0, '"SULF1"': 0.0, '"DNAJB1"': 0.0, '"FXYD3"': 0.0, '"MALRD1"': 0.0, '"FN1"': 0.0, '"MATN2"': 0.0, '"SCNN1G"': 0.0, '"CLIC3"': 0.0, '"POLD1"': 0.0, '"SORL1"': 0.0, '"ABCG2"': 0.0, '"MT-CO1"': 0.0, '"TMTC1"': 0.0, '"MAP1B"': 0.0, '"NOTCH1"': 0.0, '"PTPRH"': 0.0, '"BIRC5"': 0.0, '"MT1X"': 0.0, '"LAMB1"': 0.0, '"HSPA1B"': 0.0, '"LAMC2"': 0.0, '"TGM2"': 0.0, '"LSS"': 0.0, '"SCD"': 0.0, '"DYNC2I2"': 0.0, '"SLC3A2"': 0.0, '"MT2A"': 0.0, '"PEG13"': 0.0, '"MYH9"': 0.0, '"AGR2"': 0.0, '"PSRC1"': 0.0, '"FLNA"': 0.0, '"HMCN1"': 0.0, '"CITED2"': 0.0, '"KLF10"': 0.0, '"GADD45G"': 0.0, '"C1orf116"': 0.0, '"TSPAN1"': 0.0, '"CXCR4"': 0.0, '"PIK3IP1"': 0.0, '"PRR11"': 0.0, '"DLL1"': 0.0, '"RND1"': 0.0, '"SERPINE1"': 0.0, '"PLXNA2"': 0.0, '"RET"': 0.0, '"CAPN8"': 0.0, '"ATAD2"': 0.0, '"ADORA1"': 0.0, '"IFITM3"': 0.0, '"ISM2"': 0.0, '"WDR62"': 0.0, '"SAPCD2"': 0.0, '"MCM6"': 0.0, '"COL17A1"': 0.0, '"SCIN"': 0.0, '"HIGD1A"': 0.0, '"PRDM1"': 0.0, '"SMTN"': 0.0, '"ITGB5"': 0.0, '"KNSTRN"': 0.0, '"COL4A3"': 0.0, '"ST6GALNAC2"': 0.0, '"DHCR24"': 0.0, '"ABCC3"': 0.0, '"MMP13"': 0.0, '"IGFBP4"': 0.0, '"ZNF488"': 0.0, '"BEST1"': 0.0, '"KIF23"': 0.0, '"PCSK2"': 0.0, '"PKP1"': 0.0, '"PALLD"': 0.0, '"KLK6"': 0.0, '"COX6C"': 0.0, '"PADI4"': 0.0, '"GGT1"': 0.0, '"CCN1"': 0.0, '"PLAU"': 0.0, '"EFEMP1"': 0.0, '"OSGIN1"': 0.0, '"IRF2BP2"': 0.0, '"CDK1"': 0.0, '"DAPK2"': 0.0, '"RGL1"': 0.0, '"OLFM1"': 0.0, '"ID3"': 0.0, '"SH3BP4"': 0.0, '"FTH1"': 0.0, '"ITGB6"': 0.0, '"SELENBP1"': 0.0, '"PLK2"': 0.0, '"SEMA3B"': 0.0, '"PTGES"': 0.0, '"GRHL3"': 0.0, '"OASL"': 0.0, '"KCNG1"': 0.0, '"CAPN9"': 0.0, '"CRAT"': 0.0, '"STMN1"': 0.0, '"FADS1"': 0.0, '"CDSN"': 0.0, '"BRIP1"': 0.0, '"ADCY5"': 0.0, '"SNAI2"': 0.0, '"FOSL2"': 0.0, '"TBX3"': 0.0, '"RDH16"': 0.0, '"KRT4"': 0.0, '"LY6E"': 0.0, '"EGR1"': 0.0, '"FANCI"': 0.0, '"TSPY26P"': 0.0, '"ARRDC3"': 0.0, '"ALDOC"': 0.0, '"INPP5D"': 0.0, '"CELSR2"': 0.0, '"ZFP36L1"': 0.0, '"SUSD2"': 0.0, '"TUBG1"': 0.0, '"HCK"': 0.0, '"UNC5C"': 0.0, '"MT-ATP6"': 0.0, '"NELL2"': 0.0, '"ISYNA1"': 0.0, '"MYO7A"': 0.0, '"MRNIP"': 0.0, '"SERPINA5"': 0.0, '"RHOBTB3"': 0.0, '"FUT11"': 0.0, '"NEAT1"': 0.0, '"PTGS1"': 0.0, '"TSC22D3"': 0.0, '"ISG15"': 0.0, '"OPLAH"': 0.0, '"NPNT"': 0.0, '"CYFIP2"': 0.0, '"MYLIP"': 0.0, '"IFI6"': 0.0, '"GATA4"': 0.0, '"RASSF4"': 0.0, '"ROR2"': 0.0, '"CAPN2"': 0.0, '"IL20"': 0.0, '"DEPP1"': 0.0, '"LTBP2"': 0.0, '"LIMCH1"': 0.0, '"ECEL1"': 0.0, '"ITPRIP"': 0.0, '"POLA2"': 0.0, '"PLXNA4"': 0.0, '"CYP4F22"': 0.0, '"PADI3"': 0.0, '"PWWP3B"': 0.0, '"PRSS23"': 0.0, '"IFITM1"': 0.0, '"CHRD"': 0.0, '"VASN"': 0.0, '"ALS2CL"': 0.0, '"ZNF853"': 0.0, '"EFNA1"': 0.0, '"NCAPH"': 0.0, '"CORO1A"': 0.0, '"NOS3"': 0.0, '"NUP210"': 0.0, '"PAK6"': 0.0, '"CAVIN2"': 0.0, '"MKNK2"': 0.0, '"MST1R"': 0.0, '"SLC6A6"': 0.0, '"UPP1"': 0.0, '"SYT12"': 0.0, '"PSORS1C1"': 0.0, '"IFI27"': 0.0, '"LDLR"': 0.0, '"KIT"': 0.0, '"AHNAK2"': 0.0, '"PCDH1"': 0.0, '"ATP2A3"': 0.0, '"PODXL"': 0.0, '"L1CAM"': 0.0, '"EGFR"': 0.0, '"NFKBIA"': 0.0, '"HSPB1"': 0.0, '"ZNF319"': 0.0, '"DISP2"': 0.0, '"BRINP2"': 0.0, '"PAQR4"': 0.0, '"PDE4C"': 0.0, '"BDKRB2"': 0.0, '"COL3A1"': 0.0, '"KCTD11"': 0.0, '"KYNU"': 0.0, '"SFXN3"': 0.0, '"ANXA3"': 0.0, '"SCARA3"': 0.0, '"SARDH"': 0.0, '"TRPV6"': 0.0, '"WSCD1"': 0.0, '"UNC5B"': 0.0, '"RAP1GAP"': 0.0, '"H2BC21"': 0.0, '"KRT23"': 0.0, '"MAB21L4"': 0.0, '"ETS2"': 0.0, '"ITGAL"': 0.0, '"THBD"': 0.0, '"LRATD1"': 0.0, '"RAP2B"': 0.0, '"TSKU"': 0.0, '"AARS1"': 0.0, '"GEM"': 0.0, '"TONSL"': 0.0, '"OPRL1"': 0.0, '"CAD"': 0.0, '"PCDH7"': 0.0, '"NIBAN1"': 0.0, '"LINC01166"': 0.0, '"AQP3"': 0.0, '"SPHK1"': 0.0, '"BCL6"': 0.0, '"CGA"': 0.0, '"SFTPA2"': 0.0, '"H1-2"': 0.0, '"MID1"': 0.0, '"PXDN"': 0.0, '"BHLHE40-AS1"': 0.0, '"CLDN9"': 0.0, '"ROR1"': 0.0, '"AZIN2"': 0.0, '"FAM162A"': 0.0, '"PGLYRP2"': 0.0, '"CLDN1"': 0.0, '"HSH2D"': 0.0, '"SLC44A4"': 0.0, '"LYPD3"': 0.0, '"LOX"': 0.0, '"PLAC1"': 0.0, '"H2AX"': 0.0, '"H3C4"': 0.0, '"SYNE3"': 0.0, '"CPA4"': 0.0, '"DUSP10"': 0.0, '"FBN1"': 0.0, '"DNER"': 0.0, '"GLRA3"': 0.0, '"TRIP6"': 0.0, '"PPP1R3B"': 0.0, '"WNT9A"': 0.0, '"DOCK2"': 0.0, '"PLAUR"': 0.0, '"NR4A3"': 0.0, '"ZFP36L2"': 0.0, '"GUCY1A1"': 0.0, '"PLS3"': 0.0, '"IGHG4"': 0.0, '"RUBCNL"': 0.0, '"CDKN3"': 0.0, '"KRT86"': 0.0, '"IGFBP2"': 0.0, '"VTCN1"': 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'"ANXA6"': 0.0, '"MRC2"': 0.0, '"LGALS1"': 0.0, '"STRIP2"': 0.0, '"SLCO2A1"': 0.0, '"LCP1"': 0.0, '"GP2"': 0.0, '"NYNRIN"': 0.0, '"TIMELESS"': 0.0, '"TM4SF1"': 0.0, '"OAS3"': 0.0, '"CPEB1"': 0.0, '"ATF3"': 0.0, '"PLEKHG6"': 0.0, '"MAB21L3"': 0.0, '"TGM1"': 0.0, '"MAPKBP1"': 0.0, '"NLRC5"': 0.0, '"RNF183"': 0.0, '"TCN2"': 0.0, '"SLC38A3"': 0.0, '"TES"': 0.0, '"ASPG"': 0.0, '"NDC80"': 0.0, '"PHLDB1"': 0.0, '"RIPK4"': 0.0, '"CDKN2B"': 0.0, '"LINC00638"': 0.0, '"GTPBP2"': 0.0, '"IL1R2"': 0.0, '"KLF7"': 0.0, '"KLHL24"': 0.0, '"IER5L"': 0.0, '"PIK3R5"': 0.0, '"LINC02395"': 0.0, '"NKAIN1"': 0.0, '"RORC"': 0.0, '"TMEM30BP1"': 0.0, '"ALOXE3"': 0.0, '"VWA5B2"': 0.0, '"HS3ST3A1"': 0.0, '"TXNIP"': 0.0, '"DLL4"': 0.0, '"NHSL2"': 0.0, '"LINC01488"': 0.0, '"IFT122"': 0.0, '"IL21R"': 0.0, '"KCNK5"': 0.0, '"PHLDA3"': 0.0, '"CENPF"': 0.0, '"AEN"': 0.0, '"GREB1"': 0.0, '"ANKRD35"': 0.0, '"LINC01164"': 0.0, '"TNFRSF12A"': 0.0, '"SOX9"': 0.0, '"ADAMTS1"': 0.0, '"BTG2"': 0.0, '"ARID5A"': 0.0, '"OAS1"': 0.0, 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'"RUNX2"': 0.0, '"PLD6"': 0.0, '"COLEC10"': 0.0, '"SEPTIN6"': 0.0, '"PLXNC1"': 0.0, '"NAT8B"': 0.0, '"CCK"': 0.0, '"TYRP1"': 0.0, '"TCHH"': 0.0, '"DUSP8"': 0.0, '"PLCD4"': 0.0, '"IRAG1-AS1"': 0.0, '"CARD14"': 0.0, '"PLXNA3"': 0.0, '"B4GALNT2"': 0.0, '"GLRB"': 0.0, '"ETV5"': 0.0, '"TMEM150C"': 0.0, '"TFAP2E"': 0.0, '"ALDH2"': 0.0, '"ADGRF4"': 0.0, '"SH2D3C"': 0.0, '"SLC1A5"': 0.0, '"SREBF1"': 0.0, '"CCDC154"': 0.0, '"PLEKHO1"': 0.0, '"NAT1"': 0.0, '"SVEP1"': 0.0, '"AGR3"': 0.0, '"RN7SK"': 0.0, '"CHST11"': 0.0, '"CD55"': 0.0, '"ZNF221"': 0.0, '"FES"': 0.0, '"CCER2"': 0.0, '"PROB1"': 0.0, '"ASPM"': 0.0, '"PLCH2"': 0.0, '"MAP3K6"': 0.0, '"AFG3L1P"': 0.0, '"KRT18P7"': 0.0, '"RASSF7"': 0.0, '"BMF"': 0.0, '"GPR156"': 0.0, '"PLCD3"': 0.0, '"STAMBPL1"': 0.0, '"GAS6-DT"': 0.0, '"BCORL1"': 0.0, '"CSPG4"': 0.0, '"KSR1"': 0.0, '"C17orf107"': 0.0, '"TNRC18P1"': 0.0, '"TENM3"': 0.0, '"RBM22P13"': 0.0, '"ZNF555"': 0.0, '"MIR29B2CHG"': 0.0, '"PLA2G2A"': 0.0, '"FLOT2"': 0.0, '"ZFAT"': 0.0, '"BAIAP2L1"': 0.0, '"ENTPD1"': 0.0, '"KCTD7"': 0.0, '"BAG1"': 0.0, '"KIAA0408"': 0.0, '"ZNF763"': 0.0, '"ZNF69"': 0.0, '"TRAM2"': 0.0, '"TNS3"': 0.0, '"SLC7A11"': 0.0, '"TAS1R3"': 0.0, '"ARHGAP32"': 0.0, '"ZNF416"': 0.0, '"DIO1"': 0.0, '"ATP2C2"': 0.0, '"SPRY2"': 0.0, '"C1orf226"': 0.0, '"SAMHD1"': 0.0, '"ARHGEF19"': 0.0, '"CFAP74"': 0.0, '"SOX2"': 0.0, '"LINC02889"': 0.0, '"SLC1A4"': 0.0, '"LINC01275"': 0.0, '"FLT4"': 0.0, '"ZNF689"': 0.0, '"ADCK5"': 0.0, '"ZFP82"': 0.0, '"CLCN5"': 0.0, '"NFIA"': 0.0, '"TSPAN5-DT"': 0.0, '"NDST1"': 0.0, '"SNHG28"': 0.0, '"FBXW4P1"': 0.0, '"RNASE1"': 0.0, '"CHD2"': 0.0, '"RTEL1-TNFRSF6B"': 0.0, '"UNC13D"': 0.0, '"GAPDHP43"': 0.0, '"EIF4EBP1"': 0.0, '"KBTBD11"': 0.0, '"SLC5A5"': 0.0, '"CDH26"': 0.0, '"ABCC2"': 0.0, '"LINC01016"': 0.0, '"LINC02641"': 0.0, '"PRAP1"': 0.0, '"EPHB3"': 0.0, '"HLA-DQB2"': 0.0, '"ATP8B3"': 0.0, '"A2M-AS1"': 0.0, '"FAM186B"': 0.0, '"SEMA4A"': 0.0, '"FCGR2B"': 0.0, '"STYK1"': 0.0, '"SPATA12"': 0.0, '"ZDHHC8P1"': 0.0, '"CD320"': 0.0, '"RGMA"': 0.0, '"TNFAIP8L1"': 0.0, '"PPARGC1B"': 0.0, '"F2RL1"': 0.0, '"ERBB4"': 0.0, '"CDCA7"': 0.0, '"RAI2"': 0.0, '"ACY1"': 0.0, '"LINC01136"': 0.0, '"RASSF5"': 0.0, '"ADAMTSL4"': 0.0, '"WIPF1"': 0.0, '"LINC01144"': 0.0, '"TRIP10"': 0.0, '"ITGA2"': 0.0, '"MYCL"': 0.0, '"PTPRB"': 0.0, '"LCMT1-AS2"': 0.0, '"ATP9A"': 0.0, '"CRIP2"': 0.0, '"KIAA1549"': 0.0, '"SERPINH1P1"': 0.0, '"LZTS3"': 0.0, '"TMEM130"': 0.0, '"ZNF341"': 0.0, '"ASIC3"': 0.0, '"PAX9"': 0.0, '"FDXR"': 0.0, '"RSAD2"': 0.0, '"GSTM2"': 0.0, '"MAGED2"': 0.0, '"DBN1"': 0.0, '"KCNIP3"': 0.0, '"XPC"': 0.0, '"MT-RNR1"': 0.0, '"TNFRSF10B"': 0.0, '"MME"': 0.0, '"ST8SIA1"': 0.0, '"HEYL"': 0.0, '"ZNF778"': 0.0, '"RPSAP16"': 0.0, '"PLD1"': 0.0, '"RND2"': 0.0, '"FAT1"': 0.0, '"SLC46A2"': 0.0, '"CYP2C8"': 0.0, '"TCAP"': 0.0, '"CYB561D1"': 0.0, '"ABCC5"': 0.0, '"TFRC"': 0.0, '"PDXK"': 0.0, '"QPRT"': 0.0, '"HOXA7"': 0.0, '"INSYN2A"': 0.0, '"CD82"': 0.0, '"TFEB"': 0.0, '"KIF17"': 0.0, '"ELF4"': 0.0, '"SMG6"': 0.0, '"H2BC5"': 0.0, '"GCNT1"': 0.0, '"TMPRSS11E"': 0.0, '"KCNAB3"': 0.0, '"RANGAP1"': 0.0, '"PLA2G15"': 0.0, '"LINC00886"': 0.0, '"ANKZF1"': 0.0, '"DAGLA"': 0.0, '"HERC3"': 0.0, '"MUC1"': 0.0, '"AARS2"': 0.0, '"CLDN22"': 0.0, '"ASAP3"': 0.0, '"AGAP11"': 0.0, '"MAGEC3"': 0.0, '"CKMT2"': 0.0, '"COL9A2"': 0.0, '"KLHL15"': 0.0, '"NME1-NME2"': 0.0, '"SLC1A1"': 0.0, '"FOXP2"': 0.0, '"RAD51"': 0.0, '"MICAL2"': 0.0, '"PARP10"': 0.0, '"MGAT5B"': 0.0, '"HOXD1"': 0.0, '"TRIM46"': 0.0, '"NPR3"': 0.0, '"DAPP1"': 0.0, '"STING1"': 0.0, '"TTLL13P"': 0.0, '"RSPH4A"': 0.0, '"RPL23AP49"': 0.0, '"TMC5"': 0.0, '"ADAM2"': 0.0, '"RPA4"': 0.0, '"ZNF445"': 0.0, '"MMP28"': 0.0, '"LAMC1"': 0.0, '"IDH2"': 0.0, '"ACP5"': 0.0, '"RDH10"': 0.0, '"CDK6"': 0.0, '"SKIL"': 0.0, '"DIRAS2"': 0.0, '"ALDOA"': 0.0, '"SOWAHD"': 0.0, '"HCAR2"': 0.0, '"ARMCX4"': 0.0, '"MICAL3"': 0.0, '"COL1A1"': 0.0, '"JUP"': 0.0, '"FSD1"': 0.0, '"MEGF11"': 0.0, '"TUBBP10"': 0.0, '"CYB561A3"': 0.0, '"C1QL4"': 0.0, '"HSPA2"': 0.0, '"MPIG6B"': 0.0, '"FOXRED2"': 0.0, '"ARHGEF10L"': 0.0, '"POU3F1"': 0.0, '"ABCB6"': 0.0, '"EVPL"': 0.0, '"ARHGEF28"': 0.0, '"ADGRL2"': 0.0, '"MYCN"': 0.0, '"SNAI3"': 0.0, '"ADA"': 0.0, '"ZNF285"': 0.0, '"DDR1"': 0.0, '"CARHSP1-DT"': 0.0, '"PLEC"': 0.0, '"KDM4B"': 0.0, '"MKX"': 0.0, '"TRIP13"': 0.0, '"TMEM229A"': 0.0, '"CDA"': 0.0, '"NAT8L"': 0.0, '"ADAMTSL1"': 0.0, '"TRMT2A"': 0.0, '"DSG2"': 0.0, '"ZNF418"': 0.0, '"IRAG1"': 0.0, '"ITGB1-DT"': 0.0, '"JCADP1"': 0.0, '"HECTD3"': 0.0, '"SLC2A4"': 0.0, '"RDH13"': 0.0, '"KIAA1217"': 0.0, '"GAL3ST4"': 0.0, '"DPY19L2P2"': 0.0, '"GRN"': 0.0, '"PCDHA14"': 0.0, '"HGH1"': 0.0, '"PARP11-AS1"': 0.0, '"HEXD-IT1"': 0.0, '"BMP2K-DT"': 0.0, '"SEMA5A"': 0.0, '"SLITRK4"': 0.0, '"WDR76"': 0.0, '"BTN2A2"': 0.0, '"AFAP1L2"': 0.0, '"ADGRG2"': 0.0, '"G6PC3"': 0.0, '"RTEL1"': 0.0, '"NKD2"': 0.0, '"FERMT2"': 0.0, '"DBP"': 0.0, '"S100A13"': 0.0, '"NPHP4"': 0.0, '"MIGA2"': 0.0, '"P2RX5"': 0.0, '"LINC02666"': 0.0, '"DAAM2"': 0.0, '"SMCO3"': 0.0, '"P3H1"': 0.0, '"HNF4G"': 0.0, '"CACNB4"': 0.0, '"JAG2"': 0.0, '"CACNA2D1"': 0.0, '"GPR139"': 0.0, '"RRP12"': 0.0, '"NOP2"': 0.0, '"SHFL"': 0.0, '"PCLAF"': 0.0, '"STAG1-DT"': 0.0, '"GCNA"': 0.0, '"SYNE1"': 0.0, '"BTG1"': 0.0, '"SOCS2-AS1"': 0.0, '"ICAM2"': 0.0, '"FGF11"': 0.0, '"PPFIBP2"': 0.0, '"ASB13"': 0.0, '"SUV39H1"': 0.0, '"SLC25A34"': 0.0, '"GABBR1"': 0.0, '"OPRD1"': 0.0, '"LFNG"': 0.0, '"ELFN1"': 0.0, '"LRRC45"': 0.0, '"PBXIP1"': 0.0, '"SIM2"': 0.0, '"DNAAF8"': 0.0, '"LINC01615"': 0.0, '"TNNI2"': 0.0, '"ERVE-1"': 0.0, '"RNF43"': 0.0, '"FAM43A"': 0.0, '"TXNDC2"': 0.0, '"KCNMA1"': 0.0, '"KCNS3"': 0.0, '"LRRTM2"': 0.0, '"ZNF333"': 0.0, '"CYP2D7"': 0.0, '"CADM1"': 0.0, '"APBB2"': 0.0, '"RHPN1"': 0.0, '"PPIAP30"': 0.0, '"TRPC6"': 0.0, '"FBF1"': 0.0, '"PPP1R9A"': 0.0, '"HLA-DQB1"': 0.0, '"LSMEM1"': 0.0, '"PRR29"': 0.0, '"CLIP4"': 0.0, '"OSBPL6"': 0.0, '"RPSAP36"': 0.0, '"MPV17L2"': 0.0, '"DDX60"': 0.0, '"NAGLU"': 0.0, '"C9orf163"': 0.0, '"FOLR1"': 0.0, '"TRPV4"': 0.0, '"F5"': 0.0, '"STX18-AS1"': 0.0, '"RRM1"': 0.0, '"RPS5P3"': 0.0, '"OLFML2A"': 0.0, '"SLC14A1"': 0.0, '"EMP1"': 0.0, '"TNIK"': 0.0, '"TDRD12"': 0.0, '"KREMEN2"': 0.0, '"SLC9A4"': 0.0, '"AMZ1"': 0.0, '"C8G"': 0.0, '"SPTBN2"': 0.0, '"INPP4B"': 0.0, '"RARRES2"': 0.0, '"KLC2"': 0.0, '"ZNF783"': 0.0, '"LINC00466"': 0.0, '"CD68"': 0.0, '"TPTE2P1"': 0.0, '"REEP4"': 0.0, '"TRIB2"': 0.0, '"SNORD14C"': 0.0, '"ZNF804A"': 0.0, '"ADCY9"': 0.0, '"ZNF460"': 0.0, '"IFT140"': 0.0, '"ROBO3"': 0.0, '"NME3"': 0.0, '"TPD52L1"': 0.0, '"PKHD1L1"': 0.0, '"CGN"': 0.0, '"HSPA1L"': 0.0, '"SLC12A1"': 0.0, '"POU5F1B"': 0.0, '"GPT2"': 0.0, '"KCNK12"': 0.0, '"ZNF256"': 0.0, '"LDB3"': 0.0, '"TENT5A"': 0.0, '"HSPA7"': 0.0, '"RNA5SP155"': 0.0, '"TMPPE"': 0.0, '"C1orf216"': 0.0, '"TNFAIP8L3"': 0.0, '"FERMT1"': 0.0, '"KIF26A"': 0.0, '"ZNF587P1"': 0.0, '"PSD3"': 0.0, '"IFITM10"': 0.0, '"TMEM139"': 0.0, '"LINC01237"': 0.0, '"MXD4"': 0.0, '"TLE6"': 0.0, '"MBTPS1"': 0.0, '"ACAT2"': 0.0, '"TRANK1"': 0.0, '"IRX3"': 0.0, '"MMRN2"': 0.0, '"VPS13C-DT"': 0.0, '"TGFB3"': 0.0, '"ERBB3"': 0.0, '"ABCC1"': 0.0, '"ABCA2"': 0.0, '"COL6A2"': 0.0, '"RUSC1"': 0.0, '"USP51"': 0.0, '"ZNF551"': 0.0, '"BCL2L11"': 0.0, '"RNF224"': 0.0, '"RAB3B"': 0.0, '"S100A2"': 0.0, '"THBS1-IT1"': 0.0, '"LYG1"': 0.0, '"SLC25A29"': 0.0, '"CCDC69"': 0.0, '"SMPDL3B"': 0.0, '"ZNF792"': 0.0, '"AKR7A3"': 0.0, '"SNED1"': 0.0, '"GMFG"': 0.0, '"PEBP1"': 0.0, '"SCHIP1"': 0.0, '"OR8G3P"': 0.0, '"SLC4A3"': 0.0, '"LINC02613"': 0.0, '"PRPF19-DT"': 0.0, '"PGGHG"': 0.0, '"PAX6"': 0.0, '"PANX2"': 0.0, '"MCAM"': 0.0, '"WDR24"': 0.0, '"TPM4"': 0.0, '"RASL11B"': 0.0, '"MCC"': 0.0, '"LINC00862"': 0.0, '"IPO13"': 0.0, '"LINC02716"': 0.0, '"SLC4A10"': 0.0, '"FAM227A"': 0.0, '"LHX4"': 0.0, '"ZNF395"': 0.0, '"NINJ1"': 0.0, '"ARMH1"': 0.0, '"PGR"': 0.0, '"PGAM1P7"': 0.0, '"THOP1"': 0.0, '"NECTIN3-AS1"': 0.0, '"MMP17"': 0.0, '"SEMA4F"': 0.0, '"GPRC5C"': 0.0, '"ADHFE1"': 0.0, '"IFT172"': 0.0, '"PFKFB1"': 0.0, '"NT5CP1"': 0.0, '"PLBD1"': 0.0, '"CSMD3"': 0.0, '"KCNN2"': 0.0, '"WDR4"': 0.0, '"PPRC1"': 0.0, '"TACR2"': 0.0, '"EPHA6"': 0.0, '"ABHD14A-ACY1"': 0.0, '"DDR2"': 0.0, '"ZBTB18"': 0.0, '"PRKCZ-AS1"': 0.0, '"ADGRG1"': 0.0, '"IL12A"': 0.0, '"FREM2"': 0.0, '"HOXD10"': 0.0, '"PLA2R1"': 0.0, '"PLXNB1"': 0.0, '"FANCD2"': 0.0, '"PAX3"': 0.0, '"SBF1"': 0.0, '"COL18A1"': 0.0, '"DIRC3"': 0.0, '"TTYH1"': 0.0, '"SHROOM1"': 0.0, '"POC1A"': 0.0, '"ZFYVE26"': 0.0, '"CFAP65"': 0.0, '"RTL6"': 0.0, '"PTPRF"': 0.0, '"LRGUK"': 0.0, '"IGF2BP1"': 0.0, '"IGHEP2"': 0.0, '"KDM8"': 0.0, '"HOXD11"': 0.0, '"LMBR1L"': 0.0, '"SIPA1"': 0.0, '"KRT18P46"': 0.0, '"CTC1"': 0.0, '"RTKN"': 0.0, '"SHPK"': 0.0, '"EPS8L1"': 0.0, '"RDH12"': 0.0, '"GYG2"': 0.0, '"CNTNAP1"': 0.0, '"SARS1"': 0.0, '"KIAA2012"': 0.0, '"PAQR6"': 0.0, '"CCDC85A"': 0.0, '"MYO1E"': 0.0, '"SLC26A6"': 0.0, '"SHC3"': 0.0, '"SLC37A4"': 0.0, '"IGSF9"': 0.0, '"LINC00887"': 0.0, '"FAM222A"': 0.0, '"H6PD"': 0.0, '"LINC00607"': 0.0, '"CORO7"': 0.0, '"ST3GAL5"': 0.0, '"BDNF"': 0.0, '"TANGO2"': 0.0, '"FAAP100"': 0.0, '"SLC52A2"': 0.0, '"SOWAHB"': 0.0, '"FTH1P24"': 0.0, '"ZSCAN12P1"': 0.0, '"BCL2L14"': 0.0, '"GPHA2"': 0.0, '"ZNF84"': 0.0, '"CPEB2"': 0.0, '"CCDC33"': 0.0, '"CZIB-DT"': 0.0, '"YEATS2"': 0.0, '"TMEM255B"': 0.0, '"FAXC"': 0.0, '"XKR8"': 0.0, '"LINC00570"': 0.0, '"IMPDH1P5"': 0.0, '"OR7E91P"': 0.0, '"SNCG"': 0.0, '"SSH3"': 0.0, '"LINC02861"': 0.0, '"ZNF143"': 0.0, '"CORO2A"': 0.0, '"FCSK"': 0.0, '"MAMLD1"': 0.0, '"PM20D1"': 0.0, '"PID1"': 0.0, '"CDCA4"': 0.0, '"CFTR"': 0.0, '"AMPD3"': 0.0, '"HERPUD1"': 0.0, '"SDCBP2"': 0.0, '"SELENOP"': 0.0, '"H1-6"': 0.0, '"NCMAP"': 0.0, '"TPM1"': 0.0, '"TMEM37"': 0.0, '"TEKT3"': 0.0, '"ZNF441"': 0.0, '"ABLIM3"': 0.0, '"LY6K"': 0.0, '"IARS1"': 0.0, '"ARL4C"': 0.0, '"SGMS1-AS1"': 0.0, '"ZMYND12"': 0.0, '"RHOBTB2"': 0.0, '"PGAP3"': 0.0, '"ANKRD22"': 0.0, '"H1-5"': 0.0, '"ARL14"': 0.0, '"ADAMTS17"': 0.0, '"HRH3"': 0.0, '"NUDT11"': 0.0, '"PLA2G4C"': 0.0, '"TEDC1"': 0.0, '"PLEKHM3"': 0.0, '"SMOC2"': 0.0, '"CLDN23"': 0.0, '"TRIM34"': 0.0, '"AMTN"': 0.0, '"TESC"': 0.0, '"RTL5"': 0.0, '"LMOD1"': 0.0, '"SUSD6"': 0.0, '"TMEM163"': 0.0, '"EPHB1"': 0.0, '"TSPYL2"': 0.0, '"CCL27"': 0.0, '"TTF2"': 0.0, '"CELF6"': 0.0, '"MN1"': 0.0, '"EEF1DP3"': 0.0, '"ABAT"': 0.0, '"PKIB"': 0.0, '"AKNA"': 0.0, '"ZBTB39"': 0.0, '"FZD1"': 0.0, '"MYO15B"': 0.0, '"PIP5K1B"': 0.0, '"PLEKHN1"': 0.0, '"ZBED6CL"': 0.0, '"TSPAN33"': 0.0, '"TMEM204"': 0.0, '"PLOD1"': 0.0, '"CAMKK1"': 0.0, '"WNT3"': 0.0, '"PIANP"': 0.0, '"CD27-AS1"': 0.0, '"DNAI7"': 0.0, '"MAFG"': 0.0, '"LZTR1"': 0.0, '"BCO2"': 0.0, '"GRIK5"': 0.0, '"SLC25A27"': 0.0, '"DENND5A"': 0.0, '"CDK5R1"': 0.0, '"FAM13A-AS1"': 0.0}

Apparently, the gene that is more important in determining wether a cell is under hypoxic or normoxic condition is the NDRG1, which was fifth in the other analysis.

In [ ]:
# to see the less important ones
print({k: v for k, v in sorted(genes.items(), key=lambda item: item[1], reverse=False)})
{'"CYP1A1"': 0.0, '"DDIT4"': 0.0, '"PFKFB3"': 0.0, '"AREG"': 0.0, '"MYBL2"': 0.0, '"ADM"': 0.0, '"CDC20"': 0.0, '"KRT80"': 0.0, '"PLK1"': 0.0, '"TK1"': 0.0, '"GDF15"': 0.0, '"TFF1"': 0.0, '"KIF20A"': 0.0, '"VEGFA"': 0.0, '"BCAS1"': 0.0, '"RASD1"': 0.0, '"NR4A1"': 0.0, '"IGFBP3"': 0.0, '"SLC2A1"': 0.0, '"ITGA5"': 0.0, '"CCNB1"': 0.0, '"UBE2C"': 0.0, '"FOS"': 0.0, '"PFKFB4"': 0.0, '"CEACAM5"': 0.0, '"TGFBI"': 0.0, '"BHLHE40"': 0.0, '"LOXL2"': 0.0, '"LMCD1"': 0.0, '"BAMBI"': 0.0, '"RRM2"': 0.0, '"TUBA1B"': 0.0, '"TPX2"': 0.0, '"PRC1"': 0.0, '"CDKN1A"': 0.0, '"KPNA2"': 0.0, '"SPAG5"': 0.0, '"SPOCK1"': 0.0, '"AURKB"': 0.0, '"ANGPTL4"': 0.0, '"UGDH"': 0.0, '"ASF1B"': 0.0, '"HSPA6"': 0.0, '"FAM83D"': 0.0, '"IGFBP5"': 0.0, '"AURKA"': 0.0, '"HSPB8"': 0.0, '"PTTG1"': 0.0, '"GPRC5A"': 0.0, '"ZWINT"': 0.0, '"TIMP3"': 0.0, '"HILPDA"': 0.0, '"HMOX1"': 0.0, '"RGS16"': 0.0, '"DUSP4"': 0.0, '"PCDH10"': 0.0, '"DUSP1"': 0.0, '"DKK1"': 0.0, '"GFRA1"': 0.0, '"KIF2C"': 0.0, '"SLC7A5"': 0.0, '"PADI2"': 0.0, '"JAG1"': 0.0, '"ACKR3"': 0.0, '"TFF3"': 0.0, '"ELAPOR1"': 0.0, '"ST3GAL1"': 0.0, '"GSN"': 0.0, '"BMP7"': 0.0, '"TOP2A"': 0.0, '"UHRF1"': 0.0, '"ENO2"': 0.0, '"ANXA1"': 0.0, '"TRIB3"': 0.0, '"CCNB2"': 0.0, '"LRP4"': 0.0, '"CEACAM6"': 0.0, '"LINC00052"': 0.0, '"PREX1"': 0.0, '"GPER1"': 0.0, '"MCM7"': 0.0, '"PHLDA1"': 0.0, '"RAMP1"': 0.0, '"EDN2"': 0.0, '"DDIT3"': 0.0, '"KDM3A"': 0.0, '"CCN2"': 0.0, '"CCN5"': 0.0, '"SRF"': 0.0, '"CA9"': 0.0, '"MDK"': 0.0, '"MCM2"': 0.0, '"FEN1"': 0.0, '"TROAP"': 0.0, '"PIMREG"': 0.0, '"ARL6IP1"': 0.0, '"NUPR1"': 0.0, '"GSTM3"': 0.0, '"MCM5"': 0.0, '"NEDD9"': 0.0, '"TUBA4A"': 0.0, '"EPAS1"': 0.0, '"NTN4"': 0.0, '"SOX4"': 0.0, '"TRIM29"': 0.0, '"S100P"': 0.0, '"MKI67"': 0.0, '"IFI30"': 0.0, '"PTGER4"': 0.0, '"TRIM16"': 0.0, '"PHLDA1-AS1"': 0.0, '"KRT81"': 0.0, '"NR3C1"': 0.0, '"CASP14"': 0.0, '"EDN1"': 0.0, '"MCM3"': 0.0, '"CDC45"': 0.0, '"NR4A2"': 0.0, '"OVOL1"': 0.0, '"RECQL4"': 0.0, '"SCUBE2"': 0.0, '"E2F1"': 0.0, '"SERPINA3"': 0.0, '"SFXN2"': 0.0, 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'"TRIP10"': 0.0, '"ITGA2"': 0.0, '"MYCL"': 0.0, '"PTPRB"': 0.0, '"LCMT1-AS2"': 0.0, '"ATP9A"': 0.0, '"CRIP2"': 0.0, '"KIAA1549"': 0.0, '"SERPINH1P1"': 0.0, '"LZTS3"': 0.0, '"TMEM130"': 0.0, '"ZNF341"': 0.0, '"ASIC3"': 0.0, '"PAX9"': 0.0, '"FDXR"': 0.0, '"RSAD2"': 0.0, '"GSTM2"': 0.0, '"MAGED2"': 0.0, '"DBN1"': 0.0, '"KCNIP3"': 0.0, '"XPC"': 0.0, '"MT-RNR1"': 0.0, '"TNFRSF10B"': 0.0, '"MME"': 0.0, '"ST8SIA1"': 0.0, '"HEYL"': 0.0, '"ZNF778"': 0.0, '"RPSAP16"': 0.0, '"PLD1"': 0.0, '"RND2"': 0.0, '"FAT1"': 0.0, '"SLC46A2"': 0.0, '"CYP2C8"': 0.0, '"TCAP"': 0.0, '"CYB561D1"': 0.0, '"ABCC5"': 0.0, '"TFRC"': 0.0, '"PDXK"': 0.0, '"QPRT"': 0.0, '"HOXA7"': 0.0, '"INSYN2A"': 0.0, '"CD82"': 0.0, '"TFEB"': 0.0, '"KIF17"': 0.0, '"ELF4"': 0.0, '"SMG6"': 0.0, '"H2BC5"': 0.0, '"GCNT1"': 0.0, '"TMPRSS11E"': 0.0, '"KCNAB3"': 0.0, '"RANGAP1"': 0.0, '"PLA2G15"': 0.0, '"LINC00886"': 0.0, '"ANKZF1"': 0.0, '"DAGLA"': 0.0, '"HERC3"': 0.0, '"MUC1"': 0.0, '"AARS2"': 0.0, '"CLDN22"': 0.0, '"ASAP3"': 0.0, '"AGAP11"': 0.0, '"MAGEC3"': 0.0, '"CKMT2"': 0.0, '"COL9A2"': 0.0, '"KLHL15"': 0.0, '"NME1-NME2"': 0.0, '"SLC1A1"': 0.0, '"FOXP2"': 0.0, '"RAD51"': 0.0, '"MICAL2"': 0.0, '"PARP10"': 0.0, '"MGAT5B"': 0.0, '"HOXD1"': 0.0, '"TRIM46"': 0.0, '"NPR3"': 0.0, '"DAPP1"': 0.0, '"STING1"': 0.0, '"TTLL13P"': 0.0, '"RSPH4A"': 0.0, '"RPL23AP49"': 0.0, '"TMC5"': 0.0, '"ADAM2"': 0.0, '"RPA4"': 0.0, '"ZNF445"': 0.0, '"MMP28"': 0.0, '"LAMC1"': 0.0, '"IDH2"': 0.0, '"ACP5"': 0.0, '"RDH10"': 0.0, '"CDK6"': 0.0, '"SKIL"': 0.0, '"DIRAS2"': 0.0, '"ALDOA"': 0.0, '"SOWAHD"': 0.0, '"HCAR2"': 0.0, '"ARMCX4"': 0.0, '"MICAL3"': 0.0, '"COL1A1"': 0.0, '"JUP"': 0.0, '"FSD1"': 0.0, '"MEGF11"': 0.0, '"TUBBP10"': 0.0, '"CYB561A3"': 0.0, '"C1QL4"': 0.0, '"HSPA2"': 0.0, '"MPIG6B"': 0.0, '"FOXRED2"': 0.0, '"ARHGEF10L"': 0.0, '"POU3F1"': 0.0, '"ABCB6"': 0.0, '"EVPL"': 0.0, '"ARHGEF28"': 0.0, '"ADGRL2"': 0.0, '"MYCN"': 0.0, '"SNAI3"': 0.0, '"ADA"': 0.0, '"ZNF285"': 0.0, '"DDR1"': 0.0, '"CARHSP1-DT"': 0.0, '"PLEC"': 0.0, '"KDM4B"': 0.0, '"MKX"': 0.0, '"TRIP13"': 0.0, '"TMEM229A"': 0.0, '"CDA"': 0.0, '"NAT8L"': 0.0, '"ADAMTSL1"': 0.0, '"TRMT2A"': 0.0, '"DSG2"': 0.0, '"ZNF418"': 0.0, '"IRAG1"': 0.0, '"ITGB1-DT"': 0.0, '"JCADP1"': 0.0, '"HECTD3"': 0.0, '"SLC2A4"': 0.0, '"RDH13"': 0.0, '"KIAA1217"': 0.0, '"GAL3ST4"': 0.0, '"DPY19L2P2"': 0.0, '"GRN"': 0.0, '"PCDHA14"': 0.0, '"HGH1"': 0.0, '"PARP11-AS1"': 0.0, '"HEXD-IT1"': 0.0, '"BMP2K-DT"': 0.0, '"SEMA5A"': 0.0, '"SLITRK4"': 0.0, '"WDR76"': 0.0, '"BTN2A2"': 0.0, '"AFAP1L2"': 0.0, '"ADGRG2"': 0.0, '"G6PC3"': 0.0, '"RTEL1"': 0.0, '"NKD2"': 0.0, '"FERMT2"': 0.0, '"DBP"': 0.0, '"S100A13"': 0.0, '"NPHP4"': 0.0, '"MIGA2"': 0.0, '"P2RX5"': 0.0, '"LINC02666"': 0.0, '"DAAM2"': 0.0, '"SMCO3"': 0.0, '"P3H1"': 0.0, '"HNF4G"': 0.0, '"CACNB4"': 0.0, '"JAG2"': 0.0, '"CACNA2D1"': 0.0, '"GPR139"': 0.0, '"RRP12"': 0.0, '"NOP2"': 0.0, '"SHFL"': 0.0, '"PCLAF"': 0.0, '"STAG1-DT"': 0.0, '"GCNA"': 0.0, '"SYNE1"': 0.0, '"BTG1"': 0.0, '"SOCS2-AS1"': 0.0, '"ICAM2"': 0.0, '"FGF11"': 0.0, '"PPFIBP2"': 0.0, '"ASB13"': 0.0, '"SUV39H1"': 0.0, '"SLC25A34"': 0.0, '"GABBR1"': 0.0, '"OPRD1"': 0.0, '"LFNG"': 0.0, '"ELFN1"': 0.0, '"LRRC45"': 0.0, '"PBXIP1"': 0.0, '"SIM2"': 0.0, '"DNAAF8"': 0.0, '"LINC01615"': 0.0, '"TNNI2"': 0.0, '"ERVE-1"': 0.0, '"RNF43"': 0.0, '"FAM43A"': 0.0, '"TXNDC2"': 0.0, '"KCNMA1"': 0.0, '"KCNS3"': 0.0, '"LRRTM2"': 0.0, '"ZNF333"': 0.0, '"CYP2D7"': 0.0, '"CADM1"': 0.0, '"APBB2"': 0.0, '"RHPN1"': 0.0, '"PPIAP30"': 0.0, '"TRPC6"': 0.0, '"FBF1"': 0.0, '"PPP1R9A"': 0.0, '"HLA-DQB1"': 0.0, '"LSMEM1"': 0.0, '"PRR29"': 0.0, '"CLIP4"': 0.0, '"OSBPL6"': 0.0, '"RPSAP36"': 0.0, '"MPV17L2"': 0.0, '"DDX60"': 0.0, '"NAGLU"': 0.0, '"C9orf163"': 0.0, '"FOLR1"': 0.0, '"TRPV4"': 0.0, '"F5"': 0.0, '"STX18-AS1"': 0.0, '"RRM1"': 0.0, '"RPS5P3"': 0.0, '"OLFML2A"': 0.0, '"SLC14A1"': 0.0, '"EMP1"': 0.0, '"TNIK"': 0.0, '"TDRD12"': 0.0, '"KREMEN2"': 0.0, '"SLC9A4"': 0.0, '"AMZ1"': 0.0, '"C8G"': 0.0, '"SPTBN2"': 0.0, '"INPP4B"': 0.0, '"RARRES2"': 0.0, '"KLC2"': 0.0, '"ZNF783"': 0.0, '"LINC00466"': 0.0, '"CD68"': 0.0, '"TPTE2P1"': 0.0, '"REEP4"': 0.0, '"TRIB2"': 0.0, '"SNORD14C"': 0.0, '"ZNF804A"': 0.0, '"ADCY9"': 0.0, '"ZNF460"': 0.0, '"IFT140"': 0.0, '"ROBO3"': 0.0, '"NME3"': 0.0, '"TPD52L1"': 0.0, '"PKHD1L1"': 0.0, '"CGN"': 0.0, '"HSPA1L"': 0.0, '"SLC12A1"': 0.0, '"POU5F1B"': 0.0, '"GPT2"': 0.0, '"KCNK12"': 0.0, '"ZNF256"': 0.0, '"LDB3"': 0.0, '"TENT5A"': 0.0, '"HSPA7"': 0.0, '"RNA5SP155"': 0.0, '"TMPPE"': 0.0, '"C1orf216"': 0.0, '"TNFAIP8L3"': 0.0, '"FERMT1"': 0.0, '"KIF26A"': 0.0, '"ZNF587P1"': 0.0, '"PSD3"': 0.0, '"IFITM10"': 0.0, '"TMEM139"': 0.0, '"LINC01237"': 0.0, '"MXD4"': 0.0, '"TLE6"': 0.0, '"MBTPS1"': 0.0, '"ACAT2"': 0.0, '"TRANK1"': 0.0, '"IRX3"': 0.0, '"MMRN2"': 0.0, '"VPS13C-DT"': 0.0, '"TGFB3"': 0.0, '"ERBB3"': 0.0, '"ABCC1"': 0.0, '"ABCA2"': 0.0, '"COL6A2"': 0.0, '"RUSC1"': 0.0, '"USP51"': 0.0, '"ZNF551"': 0.0, '"BCL2L11"': 0.0, '"RNF224"': 0.0, '"RAB3B"': 0.0, '"S100A2"': 0.0, '"THBS1-IT1"': 0.0, '"LYG1"': 0.0, '"SLC25A29"': 0.0, '"CCDC69"': 0.0, '"SMPDL3B"': 0.0, '"ZNF792"': 0.0, '"AKR7A3"': 0.0, '"SNED1"': 0.0, '"GMFG"': 0.0, '"PEBP1"': 0.0, '"SCHIP1"': 0.0, '"OR8G3P"': 0.0, '"SLC4A3"': 0.0, '"LINC02613"': 0.0, '"PRPF19-DT"': 0.0, '"PGGHG"': 0.0, '"PAX6"': 0.0, '"PANX2"': 0.0, '"MCAM"': 0.0, '"WDR24"': 0.0, '"TPM4"': 0.0, '"RASL11B"': 0.0, '"MCC"': 0.0, '"LINC00862"': 0.0, '"IPO13"': 0.0, '"LINC02716"': 0.0, '"SLC4A10"': 0.0, '"FAM227A"': 0.0, '"LHX4"': 0.0, '"ZNF395"': 0.0, '"NINJ1"': 0.0, '"ARMH1"': 0.0, '"PGR"': 0.0, '"PGAM1P7"': 0.0, '"THOP1"': 0.0, '"NECTIN3-AS1"': 0.0, '"MMP17"': 0.0, '"SEMA4F"': 0.0, '"GPRC5C"': 0.0, '"ADHFE1"': 0.0, '"IFT172"': 0.0, '"PFKFB1"': 0.0, '"NT5CP1"': 0.0, '"PLBD1"': 0.0, '"CSMD3"': 0.0, '"KCNN2"': 0.0, '"WDR4"': 0.0, '"PPRC1"': 0.0, '"TACR2"': 0.0, '"EPHA6"': 0.0, '"ABHD14A-ACY1"': 0.0, '"DDR2"': 0.0, '"ZBTB18"': 0.0, '"PRKCZ-AS1"': 0.0, '"ADGRG1"': 0.0, '"IL12A"': 0.0, '"FREM2"': 0.0, '"HOXD10"': 0.0, '"PLA2R1"': 0.0, '"PLXNB1"': 0.0, '"FANCD2"': 0.0, '"PAX3"': 0.0, '"SBF1"': 0.0, '"COL18A1"': 0.0, '"DIRC3"': 0.0, '"TTYH1"': 0.0, '"SHROOM1"': 0.0, '"POC1A"': 0.0, '"ZFYVE26"': 0.0, '"CFAP65"': 0.0, '"RTL6"': 0.0, '"PTPRF"': 0.0, '"LRGUK"': 0.0, '"IGF2BP1"': 0.0, '"IGHEP2"': 0.0, '"KDM8"': 0.0, '"HOXD11"': 0.0, '"LMBR1L"': 0.0, '"SIPA1"': 0.0, '"KRT18P46"': 0.0, '"CTC1"': 0.0, '"RTKN"': 0.0, '"SHPK"': 0.0, '"EPS8L1"': 0.0, '"RDH12"': 0.0, '"GYG2"': 0.0, '"CNTNAP1"': 0.0, '"SARS1"': 0.0, '"KIAA2012"': 0.0, '"PAQR6"': 0.0, '"CCDC85A"': 0.0, '"MYO1E"': 0.0, '"SLC26A6"': 0.0, '"SHC3"': 0.0, '"SLC37A4"': 0.0, '"IGSF9"': 0.0, '"LINC00887"': 0.0, '"FAM222A"': 0.0, '"H6PD"': 0.0, '"LINC00607"': 0.0, '"CORO7"': 0.0, '"ST3GAL5"': 0.0, '"BDNF"': 0.0, '"TANGO2"': 0.0, '"FAAP100"': 0.0, '"SLC52A2"': 0.0, '"SOWAHB"': 0.0, '"FTH1P24"': 0.0, '"ZSCAN12P1"': 0.0, '"BCL2L14"': 0.0, '"GPHA2"': 0.0, '"ZNF84"': 0.0, '"CPEB2"': 0.0, '"CCDC33"': 0.0, '"CZIB-DT"': 0.0, '"YEATS2"': 0.0, '"TMEM255B"': 0.0, '"FAXC"': 0.0, '"XKR8"': 0.0, '"LINC00570"': 0.0, '"IMPDH1P5"': 0.0, '"OR7E91P"': 0.0, '"SNCG"': 0.0, '"SSH3"': 0.0, '"LINC02861"': 0.0, '"ZNF143"': 0.0, '"CORO2A"': 0.0, '"FCSK"': 0.0, '"MAMLD1"': 0.0, '"PM20D1"': 0.0, '"PID1"': 0.0, '"CDCA4"': 0.0, '"CFTR"': 0.0, '"AMPD3"': 0.0, '"HERPUD1"': 0.0, '"SDCBP2"': 0.0, '"SELENOP"': 0.0, '"H1-6"': 0.0, '"NCMAP"': 0.0, '"TPM1"': 0.0, '"TMEM37"': 0.0, '"TEKT3"': 0.0, '"ZNF441"': 0.0, '"ABLIM3"': 0.0, '"LY6K"': 0.0, '"IARS1"': 0.0, '"ARL4C"': 0.0, '"SGMS1-AS1"': 0.0, '"ZMYND12"': 0.0, '"RHOBTB2"': 0.0, '"PGAP3"': 0.0, '"ANKRD22"': 0.0, '"H1-5"': 0.0, '"ARL14"': 0.0, '"ADAMTS17"': 0.0, '"HRH3"': 0.0, '"NUDT11"': 0.0, '"PLA2G4C"': 0.0, '"TEDC1"': 0.0, '"PLEKHM3"': 0.0, '"SMOC2"': 0.0, '"CLDN23"': 0.0, '"TRIM34"': 0.0, '"AMTN"': 0.0, '"TESC"': 0.0, '"RTL5"': 0.0, '"LMOD1"': 0.0, '"SUSD6"': 0.0, '"TMEM163"': 0.0, '"EPHB1"': 0.0, '"TSPYL2"': 0.0, '"CCL27"': 0.0, '"TTF2"': 0.0, '"CELF6"': 0.0, '"MN1"': 0.0, '"EEF1DP3"': 0.0, '"ABAT"': 0.0, '"PKIB"': 0.0, '"AKNA"': 0.0, '"ZBTB39"': 0.0, '"FZD1"': 0.0, '"MYO15B"': 0.0, '"PIP5K1B"': 0.0, '"PLEKHN1"': 0.0, '"ZBED6CL"': 0.0, '"TSPAN33"': 0.0, '"TMEM204"': 0.0, '"PLOD1"': 0.0, '"CAMKK1"': 0.0, '"WNT3"': 0.0, '"PIANP"': 0.0, '"CD27-AS1"': 0.0, '"DNAI7"': 0.0, '"MAFG"': 0.0, '"LZTR1"': 0.0, '"BCO2"': 0.0, '"GRIK5"': 0.0, '"SLC25A27"': 0.0, '"DENND5A"': 0.0, '"CDK5R1"': 0.0, '"FAM13A-AS1"': 0.0, '"TNFAIP3"': 0.00017620750195430112, '"GHDC"': 0.00017620750195430145, '"LAMB2"': 0.0001762080037591038, '"KIF22"': 0.000176221804511278, '"INSYN1-AS1"': 0.00017622180451127824, '"LAMB3"': 0.00017622180451127827, '"GGN"': 0.0001762338180367698, '"SMTNL2"': 0.0001762496568590746, '"DMPK"': 0.00017624965685907517, '"SAMD4A"': 0.00017626321974148032, '"CYP1B1-AS1"': 0.00017626321974148062, '"INSYN1"': 0.00017626321974148064, '"PTPRN"': 0.00017633228840125366, '"OXER1"': 0.00017633228840125393, '"PPIF"': 0.00017633228840125393, '"TMEM109"': 0.0001764139495620991, '"HNRNPMP1"': 0.00017642907551164436, '"LARGE2"': 0.00017653825143488223, '"MUCL1"': 0.00017654077483137315, '"DSP"': 0.00017655367231638418, '"GADD45A"': 0.0001765536723163849, '"IER5"': 0.0001765536723163849, '"TGIF1"': 0.00017655367231638556, '"MOV10"': 0.00017655367231638556, '"ACAA2"': 0.00017669350573339454, '"ERRFI1"': 0.00017670619649729147, '"RAB37"': 0.00017685439560439568, '"IGSF1"': 0.00017709563164108462, '"MIR4435-2HG"': 0.00017709563164108462, '"CHDH"': 0.00017709563164108622, '"ELOVL5"': 0.00017733291298865076, '"IBSP"': 0.00017789373814041754, '"P2RY6"': 0.00017820000000000005, '"STC2"': 0.00017856000000000127, '"COTL1"': 0.00017857142857142803, '"SLC9A3R1-AS1"': 0.00017857142857142803, '"LPP"': 0.00017893217893218016, '"PLAAT4"': 0.00017933009826030926, '"ADGRG5"': 0.00017936862244897957, '"SHH"': 0.00034932463903120635, '"TST"': 0.00034932463903120635, '"KRT13"': 0.00034937888198757766, '"GCK"': 0.00034937888198757766, '"CALCR"': 0.00034948741845293566, '"BNIP3L"': 0.0003494874184529363, '"FOSL1"': 0.00034959792830857356, '"MXD1"': 0.00034965034965034965, '"LOXL1"': 0.0003496503496503497, '"IBA57-DT"': 0.0003496503496503497, '"CYP1B1"': 0.00034965034965035106, '"EMP2"': 0.00034986782770953195, '"TUBD1"': 0.0003498678277095321, '"TMEM64"': 0.0003498678277095329, '"ARMC9"': 0.00035014005602240886, '"CABLES1"': 0.00035014005602241124, '"TM7SF2"': 0.0003504672897196257, '"NECAB1"': 0.0003504672897196263, '"DCXR"': 0.00035046728971962647, '"DDX41"': 0.00035046728971962647, '"SQLE"': 0.00035084983627007644, '"TMSB10"': 0.00035123966942148633, '"RHOD"': 0.0003517823639774857, '"ADGRE2"': 0.00035233322893830145, '"RAMP3"': 0.00035233322893830254, '"IL27RA"': 0.00035294117647058837, '"EEF1GP4"': 0.0003535353535353536, '"MTATP6P1"': 0.0003568164109326319, '"ESR1"': 0.0003599424092145257, '"KRT17"': 0.0005203916428956906, '"SLC25A39"': 0.0005208333333333347, '"CD9"': 0.0005213562987564688, '"SLC9A3R1"': 0.0005219610269099912, '"TXNRD1"': 0.0005226480836236949, '"PFKP"': 0.0005262114314840362, '"HLA-C"': 0.0005269574991775217, '"GRB10"': 0.0005285412262156453, '"MVD"': 0.0006866036008544401, '"EBP"': 0.0006892507000509241, '"ERO1A"': 0.0006947660954145455, '"MUC16"': 0.0007010437762891417, '"PDK1"': 0.000863594487476328, '"FASN"': 0.0008695306377398602, '"HK2"': 0.0008727969961314983, '"MUC5AC"': 0.0008801233011419186, '"A4GALT"': 0.0010388211319290715, '"P4HA1"': 0.0017245829719825985, '"BNIP3"': 0.019128316830396595, '"MT-CYB"': 0.03893954522647767, '"MT-CO3"': 0.13425458853916902, '"GAPDH"': 0.15508077494604888, '"NDRG1"': 0.6223078526879188}

To see the differences in distribution of the gene, we plot some boxplots.

In [ ]:
Gene_Hypo = MCF7_Hypo_f_n_trans['"NDRG1"']
Gene_Hypo
Out[ ]:
"output.STAR.2_B7_Hypo_S79_Aligned.sortedByCoord.out.bam"       654
"output.STAR.2_B9_Hypo_S81_Aligned.sortedByCoord.out.bam"      1263
"output.STAR.2_C10_Hypo_S130_Aligned.sortedByCoord.out.bam"    2634
"output.STAR.2_C11_Hypo_S131_Aligned.sortedByCoord.out.bam"     540
"output.STAR.2_C8_Hypo_S128_Aligned.sortedByCoord.out.bam"      634
                                                               ... 
"output.STAR.4_H10_Hypo_S382_Aligned.sortedByCoord.out.bam"     481
"output.STAR.4_H14_Hypo_S383_Aligned.sortedByCoord.out.bam"    1052
"output.STAR.4_H7_Hypo_S379_Aligned.sortedByCoord.out.bam"     1263
"output.STAR.4_H8_Hypo_S380_Aligned.sortedByCoord.out.bam"      925
"output.STAR.4_H9_Hypo_S381_Aligned.sortedByCoord.out.bam"     1572
Name: "NDRG1", Length: 124, dtype: int64
In [ ]:
Gene_Norm = MCF7_Norm_f_n_trans['"NDRG1"']
Gene_Norm
Out[ ]:
"output.STAR.2_B3_Norm_S57_Aligned.sortedByCoord.out.bam"       0
"output.STAR.2_B4_Norm_S58_Aligned.sortedByCoord.out.bam"       1
"output.STAR.2_B5_Norm_S59_Aligned.sortedByCoord.out.bam"       0
"output.STAR.2_B6_Norm_S60_Aligned.sortedByCoord.out.bam"       0
"output.STAR.2_C1_Norm_S103_Aligned.sortedByCoord.out.bam"      0
                                                             ... 
"output.STAR.4_H1_Norm_S355_Aligned.sortedByCoord.out.bam"      0
"output.STAR.4_H3_Norm_S357_Aligned.sortedByCoord.out.bam"      0
"output.STAR.4_H4_Norm_S358_Aligned.sortedByCoord.out.bam"     54
"output.STAR.4_H5_Norm_S359_Aligned.sortedByCoord.out.bam"    243
"output.STAR.4_H6_Norm_S360_Aligned.sortedByCoord.out.bam"     62
Name: "NDRG1", Length: 126, dtype: int64
In [ ]:
Gene_Hypo.describe()
Out[ ]:
count     124.000000
mean     1203.637097
std       688.882910
min       149.000000
25%       665.250000
50%      1092.500000
75%      1573.000000
max      3884.000000
Name: "NDRG1", dtype: float64
In [ ]:
Gene_Norm.describe()
Out[ ]:
count    126.000000
mean      18.603175
std       44.026734
min        0.000000
25%        0.000000
50%        1.000000
75%       16.250000
max      296.000000
Name: "NDRG1", dtype: float64
In [ ]:
plt.figure(figsize=(16,16))
sns.boxplot(data=[Gene_Norm, Gene_Hypo])
plt.ylim(-100, 10000)
plt.xticks(ticks = [0, 1], labels=["Normoxic", "Hypoxic"])
plt.title("NDRG1")
plt.show()

We can see from the plot that the gene NDRG1 has very different distribution between the hypoxic and the normoxic cells.

We now plot the gene CYP1A1 because it was the one that, from the previous analysis, seemed more important.

In [ ]:
Gene_Hypo = MCF7_Hypo_f_n_trans['"CYP1A1"']
Gene_Hypo
Out[ ]:
"output.STAR.2_B7_Hypo_S79_Aligned.sortedByCoord.out.bam"          0
"output.STAR.2_B9_Hypo_S81_Aligned.sortedByCoord.out.bam"         79
"output.STAR.2_C10_Hypo_S130_Aligned.sortedByCoord.out.bam"      238
"output.STAR.2_C11_Hypo_S131_Aligned.sortedByCoord.out.bam"      443
"output.STAR.2_C8_Hypo_S128_Aligned.sortedByCoord.out.bam"        14
                                                               ...  
"output.STAR.4_H10_Hypo_S382_Aligned.sortedByCoord.out.bam"       86
"output.STAR.4_H14_Hypo_S383_Aligned.sortedByCoord.out.bam"     1654
"output.STAR.4_H7_Hypo_S379_Aligned.sortedByCoord.out.bam"     11274
"output.STAR.4_H8_Hypo_S380_Aligned.sortedByCoord.out.bam"       563
"output.STAR.4_H9_Hypo_S381_Aligned.sortedByCoord.out.bam"       522
Name: "CYP1A1", Length: 124, dtype: int64
In [ ]:
Gene_Norm = MCF7_Norm_f_n_trans['"CYP1A1"']
Gene_Norm
Out[ ]:
"output.STAR.2_B3_Norm_S57_Aligned.sortedByCoord.out.bam"     0
"output.STAR.2_B4_Norm_S58_Aligned.sortedByCoord.out.bam"     0
"output.STAR.2_B5_Norm_S59_Aligned.sortedByCoord.out.bam"     0
"output.STAR.2_B6_Norm_S60_Aligned.sortedByCoord.out.bam"     0
"output.STAR.2_C1_Norm_S103_Aligned.sortedByCoord.out.bam"    0
                                                             ..
"output.STAR.4_H1_Norm_S355_Aligned.sortedByCoord.out.bam"    0
"output.STAR.4_H3_Norm_S357_Aligned.sortedByCoord.out.bam"    0
"output.STAR.4_H4_Norm_S358_Aligned.sortedByCoord.out.bam"    0
"output.STAR.4_H5_Norm_S359_Aligned.sortedByCoord.out.bam"    1
"output.STAR.4_H6_Norm_S360_Aligned.sortedByCoord.out.bam"    0
Name: "CYP1A1", Length: 126, dtype: int64
In [ ]:
Gene_Hypo.describe()
Out[ ]:
count      124.000000
mean      3233.911290
std       7712.505628
min          0.000000
25%          0.000000
50%        307.000000
75%       2554.500000
max      58717.000000
Name: "CYP1A1", dtype: float64
In [ ]:
Gene_Norm.describe()
Out[ ]:
count    126.000000
mean       1.111111
std        7.706851
min        0.000000
25%        0.000000
50%        0.000000
75%        0.000000
max       78.000000
Name: "CYP1A1", dtype: float64
In [ ]:
plt.figure(figsize=(16,16))
sns.boxplot(data=[Gene_Norm, Gene_Hypo])
plt.ylim(-100, 10000)
plt.xticks(ticks = [0, 1], labels=["Normoxic", "Hypoxic"])
plt.title("CYP1A1")
plt.show()

Again, we can see that the distribution of the genes under hypoxic and normoxic condition are very much different.

Clustering Data

To better visualize the data, we performed a PCA in 2 dimensions and then used the data for K-means clustering. In such a way, we are trying to split the data in two groups and, by using different colours for hypoxic and normoxic cells, check whether the clustering assigned them correctly.

In [ ]:
from sklearn.decomposition import PCA
In [ ]:
from sklearn.cluster import KMeans
In [ ]:
def plot_data_C(X, col):
  for i in range(len(X)):
    plt.plot(X[i][0], X[i][1], 'k.', markersize=2, c=col[i])

def plot_centroids_C(centroids, weights=None, circle_color='w', cross_color='k'):
    if weights is not None:
        centroids = centroids[weights > weights.max() / 10]
    plt.scatter(centroids[:, 0], centroids[:, 1],
                marker='o', s=35, linewidths=8,
                color=circle_color, zorder=10, alpha=0.9)
    plt.scatter(centroids[:, 0], centroids[:, 1],
                marker='x', s=2, linewidths=12,
                color=cross_color, zorder=11, alpha=1)

def plot_decision_boundaries(clusterer, X, col, resolution=1000, show_centroids=True,
                             show_xlabels=True, show_ylabels=True):
    mins = X.min(axis=0) - 0.1
    maxs = X.max(axis=0) + 0.1
    xx, yy = np.meshgrid(np.linspace(mins[0], maxs[0], resolution),
                         np.linspace(mins[1], maxs[1], resolution))
    Z = clusterer.predict(np.c_[xx.ravel(), yy.ravel()])
    Z = Z.reshape(xx.shape)

    plt.contourf(Z, extent=(mins[0], maxs[0], mins[1], maxs[1]),
                cmap="Pastel2")
    plt.contour(Z, extent=(mins[0], maxs[0], mins[1], maxs[1]),
                linewidths=1, colors='k')
    plot_data_C(X, col)
    if show_centroids:
        plot_centroids_C(clusterer.cluster_centers_)

    if show_xlabels:
        plt.xlabel("$x_1$", fontsize=14)
    else:
        plt.tick_params(labelbottom=False)
    if show_ylabels:
        plt.ylabel("$x_2$", fontsize=14, rotation=0)
    else:
        plt.tick_params(labelleft=False)
In [ ]:
pcaM = PCA(n_components = 2)
MCF7_lowT = pcaM.fit_transform(MCF7_f_n.T)
MCF7_ret = pcaM.inverse_transform(MCF7_lowT)
print(MCF7_lowT.shape)
(250, 2)
In [ ]:
col = []
for c in MCF7_f_n.columns:
  if "Hypo" in c:
    col.append("r")
  else:
    col.append("b")
print(len(col))
250
In [ ]:
index = MCF7_f_n.T.index
MCF7_hyponormo = np.zeros((len(index)), dtype = 'int64')
for i in range(len(index)):
    MCF7_hyponormo[i] = not 'Hypo' in index[i] # 0 Hypo 1 Norm
In [ ]:
from sklearn import metrics
k = 2
for i in [42, 52, 28, 37, 67]:
  kmeans = KMeans(n_clusters=k, random_state=i)
  y_pred = kmeans.fit_predict(MCF7_lowT)
  mapping = {}
  for class_id in np.unique(MCF7_hyponormo):
      mode, _ = stats.mode(y_pred[MCF7_hyponormo==class_id]) # look at all samples with a given label and study what is the most common label given by the Gaussian mixture
      # print(stats.mode(y_pred[MCF7_hyponormo ==class_id]))
      mapping[mode[0]] = class_id
  mapping
  y_pred = np.array([mapping[cluster_id] for cluster_id in y_pred])
  # print(accuracy_score(y_pred, MCF7_hyponormo))
  print("fraction of correct predictions", np.sum(y_pred==MCF7_hyponormo) / len(y_pred))
  plt.figure(figsize=(8, 4))
  plot_decision_boundaries(kmeans, MCF7_lowT, col)
  plt.show()
fraction of correct predictions 0.96
fraction of correct predictions 0.96
fraction of correct predictions 0.96
fraction of correct predictions 0.96
fraction of correct predictions 0.96

We tried to use different random states to calculate an average score of our K-means clustering. We can see that it predicts correctly 96% of the data in every case, this is probably due to the fact that we have used a dataset obtained from a PCA in 2 dimensions.

In [ ]:
kmeans_iter1 = KMeans(n_clusters=2, init="random", n_init=1,
                     algorithm="full", max_iter=1, random_state=20)
kmeans_iter2 = KMeans(n_clusters=2, init="random", n_init=1,
                     algorithm="full", max_iter=2, random_state=20)
kmeans_iter3 = KMeans(n_clusters=2, init="random", n_init=1,
                     algorithm="full", max_iter=3, random_state=20)
kmeans_iter10 = KMeans(n_clusters=2, init="random", n_init=1,
                     algorithm="full", max_iter=10, random_state=20)

kmeans_iter1.fit(MCF7_lowT)
kmeans_iter2.fit(MCF7_lowT)
kmeans_iter3.fit(MCF7_lowT)
kmeans_iter10.fit(MCF7_lowT)
Out[ ]:
KMeans(algorithm='full', init='random', max_iter=10, n_clusters=2, n_init=1,
       random_state=20)
In [ ]:
plt.figure(figsize=(10, 8), tight_layout=True)

plt.subplot(321)
plot_decision_boundaries(kmeans_iter1, MCF7_lowT, col, show_xlabels=False, show_ylabels=False)
plt.title("max_iter: 1", fontsize=14)
plt.ylabel("$x_2$", fontsize=14, rotation=0)
plt.tick_params(labelbottom=False)

plt.subplot(322)
plot_decision_boundaries(kmeans_iter2, MCF7_lowT, col, show_centroids=False)
plot_centroids_C(kmeans_iter2.cluster_centers_)
plt.title("max_iter: 2", fontsize=14)

plt.subplot(323)
plot_decision_boundaries(kmeans_iter3, MCF7_lowT, col, show_centroids=False)
plot_centroids_C(kmeans_iter3.cluster_centers_)
plt.title("max_iter: 3", fontsize=14)

plt.subplot(324)
plot_decision_boundaries(kmeans_iter10, MCF7_lowT, col, show_centroids=False)
plot_centroids_C(kmeans_iter10.cluster_centers_)
plt.title("max_iter: 10", fontsize=14)

plt.show()
In [ ]:
from sklearn import metrics
k = 2
accuracy_scores = []
for i in [42, 52, 28, 37, 67]:
  kmeans = KMeans(n_clusters=k, random_state=i)
  y_pred = kmeans.fit_predict(MCF7_f_n.T)
  y_pred = np.array([mapping[cluster_id] for cluster_id in y_pred])
  print(accuracy_score(MCF7_hyponormo, y_pred))
  print("fraction of correct predictions", np.sum(y_pred==MCF7_hyponormo) / len(y_pred))
  accuracy_scores.append(accuracy_score(MCF7_hyponormo, y_pred))
0.972
fraction of correct predictions 0.972
0.972
fraction of correct predictions 0.972
0.972
fraction of correct predictions 0.972
0.968
fraction of correct predictions 0.968
0.972
fraction of correct predictions 0.972
In [ ]:
print("Average accuracy score:", sum(accuracy_scores)/len(accuracy_scores))
Average accuracy score: 0.9712

We then repeated the clustering using the dataset not processed by the PCA, obtaining a slightly higher accuracy score. This shows us that in this particular case, PCA in 2 dimensions keeps enough information from the original dataset.

In [ ]:
from sklearn.cluster import kmeans_plusplus

k = 2
accuracy_scores = []
for i in [110, 42, 66, 98, 200]:
  centroids, indices = kmeans_plusplus(MCF7_f_n.T.to_numpy(), n_clusters = 2, random_state=i)
  kmeans = KMeans(n_clusters=k, random_state=i)
  kmeans.fit(centroids)
  y_pred = kmeans.predict(MCF7_f_n.T)
  mapping = {}
  for class_id in np.unique(MCF7_hyponormo):
      mode, _ = stats.mode(y_pred[MCF7_hyponormo==class_id]) # look at all samples with a given label and study what is the most common label given by the Gaussian mixture
      # print(stats.mode(y_pred[MCF7_hyponormo ==class_id]))
      mapping[mode[0]] = class_id
  y_pred = np.array([mapping[cluster_id] for cluster_id in y_pred])
  print(accuracy_score(MCF7_hyponormo, y_pred))
  #print("fraction of correct predictions", np.sum(y_pred==MCF7_hyponormo) / len(y_pred))
  accuracy_scores.append(accuracy_score(MCF7_hyponormo, y_pred))
print("Average accuracy score:", sum(accuracy_scores)/len(accuracy_scores))
0.756
0.968
0.96
0.84
0.804
Average accuracy score: 0.8656

We finally tried to find the centroids using K-means++ and then used them to cluster the data. We can see that the result is really close to the previous case where we used K-means.

Skewness
In [ ]:
from scipy.stats import kurtosis, skew
from sklearn.preprocessing import PowerTransformer, QuantileTransformer

cnames = list(MCF7_f_n.columns)

colN = np.shape(MCF7_f_n)[1]
colN

df_skew_cells = []
for i in range(colN) :     
     v_df = MCF7_f_n[cnames[i]]
     df_skew_cells += [skew(v_df)]   
  #  df_skew_cells += [df[cnames[i]].skew()]
print("Minimum skewness:", min(df_skew_cells))
g = sns.histplot(df_skew_cells,bins=100, color="teal")
sns.set(rc={'figure.figsize':(10, 5)})
g.set(xlim = (0, None))
plt.xlabel('Skewness of single cells expression profiles - filtered and normalized df')
plt.show()
Minimum skewness: 8.475271329455568

Since the skewness tells us how much the gene expression of a single cell is normalized, by plotting the histogram of the skewness across the cells it's easy to see that most of the values are far from the origin, and in particular no value is smaller than 8.47, hence distributions are not normalized.

In [ ]:
import random
data = MCF7_f_n
f, axes = plt.subplots(2, 2, figsize=(14, 9 ), sharex=True)

r = [np.argmin(df_skew_cells), np.argmax(df_skew_cells)]
r += random.sample(range(250), 2)
sns.distplot(data.iloc[:,r[0]], color="skyblue", ax=axes[0,0], bins=200)
sns.distplot(data.iloc[:,r[1]], color="olive", ax=axes[0,1], bins=200)
sns.distplot(data.iloc[:, r[2]], color="gold", ax=axes[1,0], bins=200)
sns.distplot(data.iloc[:,r[3]], color="teal", ax=axes[1,1], bins=200)
axes[0,0].set_xlim(0,1000)
for i, ax in zip(r, axes.reshape(-1)):
    ax.text(x=0.97, y=0.97, transform=ax.transAxes, s="Skewness: %f" % data.iloc[:,i].skew(),\
        fontweight='demibold', fontsize=10, verticalalignment='top', horizontalalignment='right',\
        backgroundcolor='white', color='xkcd:poo brown')
    ax.text(x=0.97, y=0.91, transform=ax.transAxes, s="Kurtosis: %f" % data.iloc[:,i].kurt(),\
        fontweight='demibold', fontsize=10, verticalalignment='top', horizontalalignment='right',\
        backgroundcolor='white', color='xkcd:dried blood')
f.tight_layout()
plt.show()

We then plotted the distribution of the genes of 2 random cells, with the distributions of the cells with greatest and smallest skewness, and calculated their skewness and kurtosis. As a result, we immediately see that none of them has normal distribution, probably due to the sparsity of the data.

HCC1806

We now proceed to analyze the HCC1806 dataset as we did for MCF7.

Understanding the data
In [ ]:
HCC1806_f_n.head()
Out[ ]:
"output.STAR.PCRPlate1G12_Normoxia_S32_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G1_Hypoxia_S102_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G2_Hypoxia_S2_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G3_Hypoxia_S7_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G4_Hypoxia_S107_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G7_Normoxia_S118_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G8_Normoxia_S19_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G9_Normoxia_S121_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1H1_Hypoxia_S103_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1H2_Hypoxia_S3_Aligned.sortedByCoord.out.bam" ... "output.STAR.PCRPlate4G12_Normoxia_S243_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G1_Hypoxia_S193_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G2_Hypoxia_S198_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G6_Hypoxia_S232_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G7_Normoxia_S204_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H10_Normoxia_S210_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H11_Normoxia_S214_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H2_Hypoxia_S199_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H7_Normoxia_S205_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H9_Normoxia_S236_Aligned.sortedByCoord.out.bam"
"DDIT4" 0 8739 13098 2880 7777 208 750 127 10313 13523 ... 341 5545 5757 8337 2579 79 167 10186 238 60
"ANGPTL4" 48 2101 14032 356 5661 0 0 0 850 10110 ... 10 2085 698 2383 65 5 1 3147 41 0
"CALML5" 0 55 0 0 4383 1902 0 0 0 0 ... 0 1587 0 0 0 0 0 0 2867 0
"KRT14" 321 96 0 6211 0 0 5050 462 2127 0 ... 0 0 3077 529 156 2098 27 149 814 7
"CCNB1" 298 1824 1616 3 145 378 66 58 605 1444 ... 204 26 50 588 411 554 3585 1012 2207 477

5 rows × 182 columns

In [ ]:
HCC1806_f_n.describe()
HCC1806_f_n_describe = HCC1806_f_n.describe()
HCC1806_f_n_describe
Out[ ]:
"output.STAR.PCRPlate1G12_Normoxia_S32_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G1_Hypoxia_S102_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G2_Hypoxia_S2_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G3_Hypoxia_S7_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G4_Hypoxia_S107_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G7_Normoxia_S118_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G8_Normoxia_S19_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G9_Normoxia_S121_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1H1_Hypoxia_S103_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1H2_Hypoxia_S3_Aligned.sortedByCoord.out.bam" ... "output.STAR.PCRPlate4G12_Normoxia_S243_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G1_Hypoxia_S193_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G2_Hypoxia_S198_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G6_Hypoxia_S232_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G7_Normoxia_S204_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H10_Normoxia_S210_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H11_Normoxia_S214_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H2_Hypoxia_S199_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H7_Normoxia_S205_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H9_Normoxia_S236_Aligned.sortedByCoord.out.bam"
count 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.00000 3000.000000 3000.000000 3000.000000 3000.000000 ... 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000
mean 149.353000 182.303000 178.945667 168.183333 184.400000 168.87200 223.504333 156.678667 178.393333 183.545667 ... 153.646333 175.213000 188.859333 196.469333 144.678000 146.055000 162.045667 182.989000 155.877667 130.704000
std 1052.553246 871.447201 965.087457 918.214156 1267.698452 1607.97906 2453.417156 1312.696362 998.494048 1011.438386 ... 899.533313 966.105199 1246.163219 1128.887322 659.116172 649.928442 783.003904 1081.586336 887.607124 716.861167
min 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
25% 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
50% 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
75% 5.250000 33.000000 0.000000 30.000000 0.000000 0.00000 1.000000 23.000000 21.000000 0.000000 ... 25.000000 16.000000 7.000000 19.000000 18.000000 26.000000 28.000000 12.000000 3.500000 17.000000
max 39148.000000 22572.000000 21430.000000 24033.000000 32768.000000 59650.00000 109881.000000 61737.000000 32269.000000 26064.000000 ... 23857.000000 26918.000000 38157.000000 37232.000000 11028.000000 12319.000000 17681.000000 29201.000000 18969.000000 23424.000000

8 rows × 182 columns

Plotting the mean of the cells.

In [ ]:
sns.displot(data = HCC1806_f_n_describe.iloc[1], bins=50, color="teal")
plt.show()

Plotting the 75% quantile of the cells.

In [ ]:
sns.displot(data = HCC1806_f_n_describe.iloc[6], bins=50, color="teal")
plt.show()

It is nice to see how many cells have mean different than 0. Said so, because many of them have third-quantile equal to 0, it means that many genes will equal to 0.

Plotting now some informations about the genes.

In [ ]:
HCC1806_f_n_describe = HCC1806_f_n.T.describe()
HCC1806_f_n_describe
Out[ ]:
"DDIT4" "ANGPTL4" "CALML5" "KRT14" "CCNB1" "IGFBP3" "AKR1C2" "KRT6A" "NDRG1" "KRT4" ... "MST1R" "ZYG11A" "NRG1" "RBMS3" "VCPIP1" "LINC02693" "OR8B9P" "NEAT1" "ZDHHC23" "ODAD2"
count 182.000000 182.000000 182.000000 182.000000 182.000000 182.00000 182.000000 182.000000 182.000000 182.000000 ... 182.000000 182.000000 182.000000 182.000000 182.000000 182.000000 182.000000 182.000000 182.000000 182.000000
mean 4038.736264 1227.164835 398.175824 921.307692 867.087912 1271.28022 1407.873626 1729.543956 457.895604 396.637363 ... 123.302198 4.291209 138.868132 7.192308 56.675824 57.098901 0.153846 102.076923 12.236264 2.175824
std 4165.241080 1949.430648 886.985647 2387.091444 1268.359981 2810.10746 2582.400094 3709.250440 627.115448 1541.330938 ... 119.297816 11.790896 147.116950 21.864761 123.906663 86.519829 1.060835 140.866555 28.353222 8.754596
min 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000
25% 295.000000 4.250000 0.000000 13.750000 61.250000 83.00000 140.250000 313.500000 4.000000 0.000000 ... 27.500000 0.000000 36.250000 0.000000 0.000000 0.250000 0.000000 25.000000 0.000000 0.000000
50% 2729.500000 290.000000 0.000000 320.500000 299.500000 270.50000 484.000000 737.000000 143.500000 0.000000 ... 98.500000 0.000000 97.000000 0.000000 36.000000 34.000000 0.000000 57.000000 0.000000 0.000000
75% 6933.500000 1857.750000 465.750000 1029.000000 988.500000 1163.50000 1472.000000 1774.000000 688.750000 0.000000 ... 185.750000 0.000000 191.000000 6.000000 74.250000 68.000000 0.000000 117.500000 11.500000 0.000000
max 16700.000000 14032.000000 5482.000000 28680.000000 6914.000000 21554.00000 20195.000000 41946.000000 3356.000000 9902.000000 ... 751.000000 68.000000 852.000000 246.000000 1545.000000 615.000000 11.000000 966.000000 222.000000 67.000000

8 rows × 3000 columns

Plotting the mean of the genes.

In [ ]:
sns.displot(data = HCC1806_f_n_describe.iloc[1], bins=500, color="teal")
plt.xlim(-100, 2500)
plt.show()

Plotting the 75% quantile of the cells.

In [ ]:
sns.displot(data = HCC1806_f_n_describe.iloc[6], bins=500, color="teal")
plt.xlim(-100, 2500)
plt.show()

Many genes have both mean and 75% quantile near to 0.

Correlation
In [ ]:
# To see the correlation between genes
df_new = HCC1806_f_n.transpose().iloc[:,:25]
plt.figure(figsize=(25,25))
sns.heatmap(df_new.corr(),cbar=True,annot=True,cmap='Blues')
plt.show()
Hypo vs Norm
In [ ]:
HCC1806_Hypo_f_n = HCC1806_f_n.loc[:, HCC1806_f_n.columns.str.contains('Hypoxia')]
HCC1806_Hypo_f_n
Out[ ]:
"output.STAR.PCRPlate1G1_Hypoxia_S102_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G2_Hypoxia_S2_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G3_Hypoxia_S7_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G4_Hypoxia_S107_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1H1_Hypoxia_S103_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1H2_Hypoxia_S3_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1H5_Hypoxia_S10_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1H6_Hypoxia_S16_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate2A1_Hypoxia_S129_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate2A3_Hypoxia_S36_Aligned.sortedByCoord.out.bam" ... "output.STAR.PCRPlate4E2_Hypoxia_S196_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4E3_Hypoxia_S227_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4F1_Hypoxia_S224_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4F2_Hypoxia_S197_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4F4_Hypoxia_S228_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4F5_Hypoxia_S229_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G1_Hypoxia_S193_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G2_Hypoxia_S198_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G6_Hypoxia_S232_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H2_Hypoxia_S199_Aligned.sortedByCoord.out.bam"
"DDIT4" 8739 13098 2880 7777 10313 13523 6181 2796 6901 12430 ... 5350 5153 3661 1680 6757 3717 5545 5757 8337 10186
"ANGPTL4" 2101 14032 356 5661 850 10110 1883 2417 5228 1745 ... 1571 2936 3418 836 3435 2500 2085 698 2383 3147
"CALML5" 55 0 0 4383 0 0 836 1831 0 752 ... 0 393 0 0 872 0 1587 0 0 0
"KRT14" 96 0 6211 0 2127 0 0 51 126 0 ... 2 0 20 1 1963 111 0 3077 529 149
"CCNB1" 1824 1616 3 145 605 1444 67 301 45 536 ... 1705 120 24 95 37 1447 26 50 588 1012
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
"LINC02693" 68 0 1 0 79 0 29 73 1 0 ... 0 47 0 23 9 0 68 116 27 43
"OR8B9P" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"NEAT1" 213 92 1 128 157 53 41 52 15 29 ... 58 48 46 17 67 13 163 5 19 113
"ZDHHC23" 0 0 0 0 35 0 0 0 4 0 ... 0 1 23 0 17 0 0 0 38 0
"ODAD2" 0 0 0 0 0 0 0 0 0 7 ... 0 24 0 0 0 0 0 0 0 0

3000 rows × 97 columns

In [ ]:
HCC1806_Norm_f_n = HCC1806_f_n.loc[:, HCC1806_f_n.columns.str.contains('Normoxia')]
HCC1806_Norm_f_n
Out[ ]:
"output.STAR.PCRPlate1G12_Normoxia_S32_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G7_Normoxia_S118_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G8_Normoxia_S19_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1G9_Normoxia_S121_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate1H9_Normoxia_S122_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate2A10_Normoxia_S153_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate2A8_Normoxia_S151_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate2A9_Normoxia_S53_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate2B11_Normoxia_S159_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate2B8_Normoxia_S152_Aligned.sortedByCoord.out.bam" ... "output.STAR.PCRPlate4F12_Normoxia_S242_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4F7_Normoxia_S203_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4F9_Normoxia_S235_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G10_Normoxia_S209_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G12_Normoxia_S243_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4G7_Normoxia_S204_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H10_Normoxia_S210_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H11_Normoxia_S214_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H7_Normoxia_S205_Aligned.sortedByCoord.out.bam" "output.STAR.PCRPlate4H9_Normoxia_S236_Aligned.sortedByCoord.out.bam"
"DDIT4" 0 208 750 127 404 121 467 179 504 292 ... 369 198 314 0 341 2579 79 167 238 60
"ANGPTL4" 48 0 0 0 32 0 1 1 1 24 ... 28 18 13 0 10 65 5 1 41 0
"CALML5" 0 1902 0 0 0 163 0 490 179 2676 ... 0 0 0 0 0 0 0 0 2867 0
"KRT14" 321 0 5050 462 1893 283 1289 1 13 398 ... 1557 1122 3565 62 0 156 2098 27 814 7
"CCNB1" 298 378 66 58 2796 989 75 1658 199 3733 ... 822 962 175 875 204 411 554 3585 2207 477
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
"LINC02693" 29 1 0 195 160 24 207 196 0 8 ... 6 1 39 0 148 1 34 53 0 25
"OR8B9P" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"NEAT1" 29 56 415 42 30 44 34 10 70 102 ... 72 4 34 86 268 4 24 177 13 13
"ZDHHC23" 0 0 0 18 23 0 0 0 74 0 ... 0 0 0 0 0 145 0 53 5 4
"ODAD2" 0 0 0 0 0 0 0 0 0 0 ... 15 0 0 36 0 0 0 0 0 0

3000 rows × 85 columns

In [ ]:
df_small = HCC1806_Norm_f_n.transpose().iloc[0:, :50]
plt.figure(figsize=(16,4))
plot=sns.violinplot(data=df_small,palette="Set3",cut=0)
plt.setp(plot.get_xticklabels(), rotation=90)
plt.show()
In [ ]:
df_small = HCC1806_Hypo_f_n.transpose().iloc[0:, :50]
plt.figure(figsize=(16,4))
plot=sns.violinplot(data=df_small,palette="Set3",cut=0)
plt.setp(plot.get_xticklabels(), rotation=90)
plt.show()

Even though it is not as clear as in the MCF7 case, we can still see that there are some differences between the distibutions of genes in hypoxic or normoxic conditions.

We compute again the ration of the log_2 of the means + 1 to see what genes are more imporant than othern in classifying the hypoxic and normoxic condition. Later we also compute it with random forests.

In [ ]:
HCC1806_Hypo_f_n_trans = HCC1806_Hypo_f_n.T
HCC1806_Norm_f_n_trans = HCC1806_Norm_f_n.T
In [ ]:
HCC1806_Hypo_f_n_trans_d = HCC1806_Hypo_f_n.T.describe()
HCC1806_Norm_f_n_trans_d = HCC1806_Norm_f_n.T.describe()
In [ ]:
HCC1806_f_n_logratio = np.log2(HCC1806_Hypo_f_n_trans_d.iloc[1] + 1) - np.log2(HCC1806_Norm_f_n_trans_d.iloc[1] + 1)
HCC1806_f_n_logratio.sort_values(ascending=False)
Out[ ]:
"CA9"        6.419824
"EGLN3"      5.897350
"ANGPTL4"    5.567300
"CEACAM5"    5.416698
"TPPP3"      4.929030
               ...   
"NLRP7"     -2.387323
"RBPMS2"    -2.498775
"AKR1B10"   -2.557506
"NPFFR2"    -2.596755
"OASL"      -4.030607
Name: mean, Length: 3000, dtype: float64

Apparently, the gene CA9 is the most important in the HCC1806 dataset.

Check with random forest which cells have higher importance

We now try to get the most important genes with a random forest to check wheter they are the same as the ones we found before.

In [ ]:
data_test = HCC1806_f_n
In [ ]:
# Let's load the packages
import numpy as np
import pandas as pd
from sklearn.datasets import load_boston
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestRegressor
from sklearn.inspection import permutation_importance
#import shap
from matplotlib import pyplot as plt

plt.rcParams.update({'figure.figsize': (12.0, 8.0)})
plt.rcParams.update({'font.size': 14})
In [ ]:
index = data_test.T.index
y = np.zeros((len(index)),dtype = 'int64')
for i in range(len(index)):
    y[i] = not 'Hypo' in index[i] # 0 Hypo 1 Norm
In [ ]:
X_train, X_test, y_train, y_test = train_test_split(data_test.T, y, test_size= 0.1, random_state= 42)
In [ ]:
rf = RandomForestRegressor(n_estimators=100)
rf.fit(X_train, y_train)
Out[ ]:
RandomForestRegressor()
In [ ]:
genes_importance = rf.feature_importances_
In [ ]:
genes = {}
for n, g in zip(data_test.index, genes_importance):
  genes[n] = g
print({k: v for k, v in sorted(genes.items(), key=lambda item: item[1], reverse=True)})
{'"PGK1"': 0.41121140437726483, '"DDIT4"': 0.21375320859702115, '"NDRG1"': 0.09159165949503784, '"EGLN3"': 0.05617846108839006, '"BNIP3"': 0.03737047723028583, '"ANGPTL4"': 0.03573394372296992, '"CA9"': 0.019256528360955545, '"BNIP3L"': 0.018178378198055508, '"FUT11"': 0.017783749905413676, '"ERO1A"': 0.009754628932711123, '"BHLHE40"': 0.009046375862947207, '"INSIG1"': 0.002550127433425332, '"PFKFB3"': 0.002129661023551652, '"KDM5B"': 0.00212678801708075, '"UGT1A6"': 0.0020905611731218375, '"ENO2"': 0.001985921212941655, '"PPIF"': 0.001925520722112464, '"FAM162A"': 0.00190783790465825, '"ZFYVE1"': 0.0018494232625559577, '"F3"': 0.0016865150616515079, '"KLHL24"': 0.0016755120577069164, '"CD44"': 0.001577551533433888, '"MUC1"': 0.001434924295836034, '"IL17RD"': 0.0014321312523344835, '"CDK2AP2"': 0.0011932703760057328, '"FTL"': 0.0011852123210050725, '"PLAU"': 0.0009690943944272136, '"ZNF143"': 0.0009582549246039886, '"SLC2A3"': 0.0009576672468065446, '"RNASE7"': 0.0009555804259806406, '"SLCO4A1"': 0.0009552692573341235, '"DCLK1"': 0.0009492422738402486, '"SYTL3"': 0.0009408369408369415, '"ZNF416"': 0.0009408369408369409, '"SVEP1"': 0.0009378596087456847, '"ANTXR2"': 0.0009376688063418569, '"TMSB4X"': 0.0009351692484222606, '"MRNIP"': 0.0009116615405572046, '"LAMC1"': 0.0007303711840888068, '"TXNRD1"': 0.0007278059061337649, '"PIP5K1A"': 0.0007276785714285704, '"IL24"': 0.0007269818213811973, '"SQSTM1"': 0.0007244730656025917, '"LRRC37A15P"': 0.0007200218383958704, '"PSAP"': 0.0007194132537158435, '"CEMIP2"': 0.00071800656070319, '"FYB1"': 0.0007164835164835165, '"GLRA3"': 0.0007164835164835161, '"BTG2"': 0.0007162121212121224, '"GLRX"': 0.0007137656691849914, '"NRP1"': 0.0007131754758898458, '"LINC02709"': 0.0007116626794258369, '"NRCAM"': 0.0007114797031863813, '"VCPIP1"': 0.0007107558139534864, '"SLC2A1"': 0.0007104052850299528, '"LINC02693"': 0.0007102396514161218, '"THEMIS2"': 0.00070993031358885, '"EGLN1"': 0.0007098272608506315, '"ALDOC"': 0.0007096135218380296, '"MCM4"': 0.0007095480840827079, '"GPX2"': 0.0007092563291139227, '"EGR1"': 0.0004987165737511152, '"ALDOA"': 0.0004937850860999877, '"RAET1L"': 0.0004898817872169915, '"EHF"': 0.0004884626910398547, '"SLC7A8"': 0.0004882318485582683, '"IL1RAPL1"': 0.00048559111690796503, '"LAMP3"': 0.0004848219753302423, '"ADAMTS1"': 0.0004827134986225896, '"LAMA3"': 0.000482584465343086, '"IMPDH1P10"': 0.0004824524312896407, '"KRT19"': 0.0004822175059489343, '"ZNF333"': 0.00048161128027511215, '"PLOD2"': 0.0004811097992916174, '"SLC2A12"': 0.00048094098883572425, '"C14orf132"': 0.00048094098883572425, '"HBP1"': 0.0004807676767676759, '"PPP1R3B"': 0.00048023664176114194, '"MMP1"': 0.00048013485937361373, '"PLAC8"': 0.0004797007410559169, '"ANXA3"': 0.0004797007410559169, '"CASTOR2"': 0.0004797007410559159, '"ALOXE3"': 0.00047956313327018657, '"FAM47E"': 0.0004792561620558642, '"DEGS2"': 0.00047909656959430676, '"NQO1"': 0.00047884489685005383, '"BCL6"': 0.0004788448968500537, '"BRD2"': 0.0004788412910902879, '"KYNU"': 0.00047882283822037056, '"SH3TC2-DT"': 0.00047869710521522216, '"ID3"': 0.0004786897590361453, '"ISG15"': 0.000478545618789522, '"SFN"': 0.0004783902972644367, '"TPPP"': 0.000250566539226333, '"SLFN5"': 0.0002467985168536302, '"HSPA5"': 0.0002460748792270532, '"SLC16A2"': 0.00024607487922705313, '"KRT18"': 0.00024598372912979795, '"PEX5"': 0.0002446499191946693, '"PFKFB4"': 0.0002446030827277209, '"CRY2"': 0.0002441632231404959, '"PXN"': 0.00024413096482062003, '"MT1X"': 0.00024413096482062003, '"LHX4"': 0.00024405725950669608, '"H3C6"': 0.00024367676767676622, '"RRM2"': 0.0002436549473121457, '"TDRD7"': 0.00024358655043586552, '"SPATA18"': 0.0002433198984923121, '"SLC6A17"': 0.00024328699964178634, '"H4C3"': 0.00024325332670065906, '"IL1A"': 0.00024321885202283872, '"AKR1C2"': 0.00024319010480534982, '"PCSK5"': 0.00024314446958208048, '"WTAPP1"': 0.00024295245678513576, '"SERPINB5"': 0.00024292537527831624, '"COX6B2"': 0.00024289011248614372, '"LINC02561"': 0.00024289011248614372, '"SRXN1"': 0.0002428672103090708, '"TBX5-AS1"': 0.0002428672103090708, '"BLNK"': 0.0002425974296579081, '"MIF-AS1"': 0.00024255952380952382, '"FAM13A"': 0.00024252431412396657, '"SCIN"': 0.00024248079627826468, '"CDKN1A"': 0.00024248079627826405, '"GLIPR2"': 0.0002424512866279943, '"HCP5"': 0.00024241522903033954, '"GPT2"': 0.0002424152290303395, '"TNFRSF9"': 0.00024241340361445783, '"PLA2G4A"': 0.0002423782811216315, '"SH3BP5L"': 0.00024237828112163147, '"UCP2"': 0.0002423404095152063, '"ELFN1"': 0.000242340409515206, '"AOC2"': 0.00024230157913393362, '"SNAI2"': 0.0002079506021637069, '"MAGED1"': 0.0001846118997281788, '"CALML5"': 0.0, '"KRT14"': 0.0, '"CCNB1"': 0.0, '"IGFBP3"': 0.0, '"KRT6A"': 0.0, '"KRT4"': 0.0, '"FN1"': 0.0, '"KRT13"': 0.0, '"KRT17"': 0.0, '"LAMC2"': 0.0, '"KIF20A"': 0.0, '"SPP1"': 0.0, '"G0S2"': 0.0, '"LRRC38"': 0.0, '"CDK1"': 0.0, '"TMPRSS4"': 0.0, '"PLK1"': 0.0, '"CDC20"': 0.0, '"AURKA"': 0.0, '"PLIN2"': 0.0, '"DHRS9"': 0.0, '"MAGEC2"': 0.0, '"UBE2C"': 0.0, '"UPK1B"': 0.0, '"CYP1B1"': 0.0, '"AKR1C1"': 0.0, '"FOS"': 0.0, '"CCNE1"': 0.0, '"TOP2A"': 0.0, '"LAMB3"': 0.0, '"LY6D"': 0.0, '"S100A14"': 0.0, '"AKR1C3"': 0.0, '"CYP1B1-AS1"': 0.0, '"TPX2"': 0.0, '"CEACAM6"': 0.0, '"ALDH1A1"': 0.0, '"FAM83D"': 0.0, '"DEPP1"': 0.0, '"SERPINB2"': 0.0, '"CCNB3"': 0.0, '"CXCL1"': 0.0, '"MUC16"': 0.0, '"VILL"': 0.0, '"KLK10"': 0.0, '"ELF3"': 0.0, '"GDF15"': 0.0, '"SERPINE1"': 0.0, '"PADI3"': 0.0, '"FAM83A"': 0.0, '"CPA4"': 0.0, '"UCA1"': 0.0, '"SCD"': 0.0, '"IGFL2-AS1"': 0.0, '"TXNIP"': 0.0, '"ZNF792"': 0.0, '"PIF1"': 0.0, '"DTL"': 0.0, '"THBS1"': 0.0, '"AMIGO1"': 0.0, '"HAS2"': 0.0, '"FST"': 0.0, '"DUSP1"': 0.0, '"GJB2"': 0.0, '"CES1"': 0.0, '"AURKB"': 0.0, '"CEACAM5"': 0.0, '"CLDN8"': 0.0, '"SLPI"': 0.0, '"VIM"': 0.0, '"FTH1"': 0.0, '"GPRC5A"': 0.0, '"MEST"': 0.0, '"HJURP"': 0.0, '"NUSAP1"': 0.0, '"CCNB2"': 0.0, '"KPNA2"': 0.0, '"PLK2"': 0.0, '"LINC01559"': 0.0, '"BEST1"': 0.0, '"TGM2"': 0.0, '"DKK1"': 0.0, '"PCSK9"': 0.0, '"KCTD11"': 0.0, '"ABCA12"': 0.0, '"CCNE2"': 0.0, '"FXYD3"': 0.0, '"CLDN4"': 0.0, '"SPRR1B"': 0.0, '"MAB21L3"': 0.0, '"GRHL3"': 0.0, '"IL1RN"': 0.0, '"C2orf16"': 0.0, '"PPFIBP2"': 0.0, '"TMEM45B"': 0.0, '"MMP10"': 0.0, '"FLNA"': 0.0, '"RASSF4"': 0.0, '"ARSI"': 0.0, '"NECTIN4"': 0.0, '"ZNF285"': 0.0, '"PIMREG"': 0.0, '"PADI2"': 0.0, '"PLAT"': 0.0, '"SDHA"': 0.0, '"EPHB6"': 0.0, '"SCEL"': 0.0, '"HEPHL1"': 0.0, '"CYP4F3"': 0.0, '"KIF23"': 0.0, '"TRIB3"': 0.0, '"TNC"': 0.0, '"KCNMA1"': 0.0, '"KRT5"': 0.0, '"SLC43A3"': 0.0, '"CCN2"': 0.0, '"SERPINB10"': 0.0, '"KRT16"': 0.0, '"SLC6A8"': 0.0, '"GPNMB"': 0.0, '"GGT6"': 0.0, '"KIF1A"': 0.0, '"CLCA2"': 0.0, '"FBLN2"': 0.0, '"KIF2C"': 0.0, '"MB"': 0.0, '"LOXL2"': 0.0, '"THY1"': 0.0, '"TRBC2"': 0.0, '"S100A9"': 0.0, '"GJB6"': 0.0, '"MOCS1"': 0.0, '"TENT5C"': 0.0, '"LVRN"': 0.0, '"KLK5"': 0.0, '"MXRA5"': 0.0, '"ABCG1"': 0.0, '"MUC20"': 0.0, '"HMGB2"': 0.0, '"VCAN"': 0.0, '"IVL"': 0.0, '"FABP4"': 0.0, '"IGF2BP1"': 0.0, '"PNMA2"': 0.0, '"TCN1"': 0.0, '"AKR1B1"': 0.0, '"LCK"': 0.0, '"KCNS1"': 0.0, '"ARL6IP1"': 0.0, '"CALHM3"': 0.0, '"CHAC1"': 0.0, '"SPOCK1"': 0.0, '"GAS6"': 0.0, '"S100P"': 0.0, '"SPTSSB"': 0.0, '"KIT"': 0.0, '"NEDD9"': 0.0, '"MYO7B"': 0.0, '"TNFSF18"': 0.0, '"KLHDC8B"': 0.0, '"CYP4F12"': 0.0, '"CFB"': 0.0, '"FBP1"': 0.0, '"AKR1B10"': 0.0, '"TCIM"': 0.0, '"NPR2"': 0.0, '"SQLE"': 0.0, '"IL22RA1"': 0.0, '"AXL"': 0.0, '"H2AC6"': 0.0, '"OASL"': 0.0, '"STC1"': 0.0, '"SPAG5"': 0.0, '"NYNRIN"': 0.0, '"DHRS2"': 0.0, '"CYP2T1P"': 0.0, '"GRAMD2A"': 0.0, '"ATP8B2"': 0.0, '"OAS1"': 0.0, '"ABCC2"': 0.0, '"TNFRSF8"': 0.0, '"CYP4F11"': 0.0, '"TMPRSS11E"': 0.0, '"ADAM8"': 0.0, '"CCDC87"': 0.0, '"MYBL2"': 0.0, '"ZMYND10"': 0.0, '"TSPAN7"': 0.0, '"ADGRL2"': 0.0, '"MFAP3L"': 0.0, '"SUSD5"': 0.0, '"SLC52A1"': 0.0, '"PLEKHB1"': 0.0, '"IL20RA"': 0.0, '"MAP1A"': 0.0, '"TIMP3"': 0.0, '"NAV2"': 0.0, '"VIPR1"': 0.0, '"RGS4"': 0.0, '"SDCBP2"': 0.0, '"CHST2"': 0.0, '"CDH6"': 0.0, '"ARNT2"': 0.0, '"NFKBIA"': 0.0, '"CSTB"': 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0.0, '"LINC02643"': 0.0, '"PDLIM2"': 0.0, '"FAM53C"': 0.0, '"MEF2C"': 0.0, '"FOXL2NB"': 0.0, '"CA14"': 0.0, '"RSPH1"': 0.0, '"SLC1A2"': 0.0, '"LINC01293"': 0.0, '"LTB4R"': 0.0, '"GPM6B"': 0.0, '"PTCSC2"': 0.0, '"KCNH3"': 0.0, '"PRR18"': 0.0, '"ACTG1P10"': 0.0, '"GYS1"': 0.0, '"CDON"': 0.0, '"MROCKI"': 0.0, '"TCP11L2"': 0.0, '"ZNF862"': 0.0, '"RASSF10-DT"': 0.0, '"ICAM2"': 0.0, '"FBXL21P"': 0.0, '"VIM-AS1"': 0.0, '"ACAD10"': 0.0, '"COL16A1"': 0.0, '"SCN8A"': 0.0, '"PAM"': 0.0, '"B3GNT3"': 0.0, '"GRM4"': 0.0, '"SLC22A1"': 0.0, '"UGDH"': 0.0, '"ZNF420"': 0.0, '"VIRMA-DT"': 0.0, '"DIXDC1"': 0.0, '"CSF1"': 0.0, '"BTN2A1"': 0.0, '"SLC51B"': 0.0, '"LINC00853"': 0.0, '"ACOT11"': 0.0, '"KLF10"': 0.0, '"CYP2S1"': 0.0, '"ZNF304"': 0.0, '"RAPGEF5"': 0.0, '"FBXO10"': 0.0, '"PHGDH"': 0.0, '"GLCCI1"': 0.0, '"WDR17"': 0.0, '"LINC01852"': 0.0, '"NEURL2"': 0.0, '"PRPH"': 0.0, '"RASIP1"': 0.0, '"VSIG2"': 0.0, '"MAGI2"': 0.0, '"AJUBA"': 0.0, '"RN7SL809P"': 0.0, '"CASP10"': 0.0, '"LINC01679"': 0.0, 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'"TRPS1"': 0.0, '"BCORL1"': 0.0, '"SYNPO"': 0.0, '"THRB-AS1"': 0.0, '"TTC12"': 0.0, '"HMGB1P49"': 0.0, '"TRIM36"': 0.0, '"CLIC2"': 0.0, '"ITGB5"': 0.0, '"ID2"': 0.0, '"CELSR3"': 0.0, '"HYDIN"': 0.0, '"ADCY1"': 0.0, '"NT5E"': 0.0, '"SLC22A3"': 0.0, '"BCL2L15"': 0.0, '"PSMD2"': 0.0, '"ADSS1"': 0.0, '"TMEM263-DT"': 0.0, '"UGT1A10"': 0.0, '"TIGD3"': 0.0, '"KRTAP20-4"': 0.0, '"GAPDHP14"': 0.0, '"LINC01556"': 0.0, '"SLC27A6"': 0.0, '"PLXNB3"': 0.0, '"MKX"': 0.0, '"DNER"': 0.0, '"ITPRID2-DT"': 0.0, '"PHBP12"': 0.0, '"TTYH1"': 0.0, '"ULBP1"': 0.0, '"FZD1"': 0.0, '"EEF1DP3"': 0.0, '"IL12A"': 0.0, '"RARB"': 0.0, '"BCL11B"': 0.0, '"NUP188"': 0.0, '"SBK1"': 0.0, '"LARP4P"': 0.0, '"AFG1L"': 0.0, '"SEC24D"': 0.0, '"JARID2-DT"': 0.0, '"PDGFB"': 0.0, '"HSP90AA1"': 0.0, '"PTN"': 0.0, '"ACSL1"': 0.0, '"C20orf144"': 0.0, '"TWSG1-DT"': 0.0, '"PTHLH"': 0.0, '"FNDC11"': 0.0, '"WIPF3"': 0.0, '"MRPS31P5"': 0.0, '"EPHA2"': 0.0, '"DYNLT2"': 0.0, '"ZNF493"': 0.0, '"ZNF134"': 0.0, '"SORCS2"': 0.0, '"AGER"': 0.0, '"ASNS"': 0.0, '"REEP1"': 0.0, '"LINC01213"': 0.0, '"ALDH1A3-AS1"': 0.0, '"RNF207-AS1"': 0.0, '"SMIM18"': 0.0, '"EIF4E3"': 0.0, '"CKB"': 0.0, '"FURIN"': 0.0, '"NSG1"': 0.0, '"IGF2"': 0.0, '"MYLK4"': 0.0, '"DLEU2L"': 0.0, '"CLYBL"': 0.0, '"NF1P8"': 0.0, '"LINC02614"': 0.0, '"SLC16A10"': 0.0, '"PGAP3"': 0.0, '"ALOX5"': 0.0, '"MT-ND5"': 0.0, '"PRSS27"': 0.0, '"ZFAT"': 0.0, '"SRM"': 0.0, '"ERVMER34-1"': 0.0, '"HSPH1"': 0.0, '"PLXNA2"': 0.0, '"UCHL1-DT"': 0.0, '"PLEKHG6"': 0.0, '"RPS23P1"': 0.0, '"ANXA6"': 0.0, '"NET1"': 0.0, '"PAIP1P1"': 0.0, '"TNFRSF11A"': 0.0, '"IRAK1"': 0.0, '"AARSD1P1"': 0.0, '"ERFE"': 0.0, '"TULP2"': 0.0, '"PGF"': 0.0, '"ZNF566-AS1"': 0.0, '"SLCO1C1"': 0.0, '"NFE2L1-DT"': 0.0, '"CLDN11"': 0.0, '"RFWD3"': 0.0, '"COL8A1"': 0.0, '"TMEM150A"': 0.0, '"SGPP2"': 0.0, '"MAP3K6"': 0.0, '"FOXD2"': 0.0, '"HCG15"': 0.0, '"CA7"': 0.0, '"KLRG2"': 0.0, '"NLRP1"': 0.0, '"ACTN1-DT"': 0.0, '"COL28A1"': 0.0, '"ARFGEF1-DT"': 0.0, '"SLFN11"': 0.0, '"SCART1"': 0.0, '"TMCC1-DT"': 0.0, '"HLA-T"': 0.0, '"ETV7"': 0.0, '"DYDC2"': 0.0, '"CABLES1"': 0.0, '"MARCHF4"': 0.0, '"CEMIP"': 0.0, '"SGSM3"': 0.0, '"UBE2T"': 0.0, '"ABCC4"': 0.0, '"NPIPB2"': 0.0, '"BAG3"': 0.0, '"HRK"': 0.0, '"BMP2K-DT"': 0.0, '"ZNF736"': 0.0, '"ACVR2B"': 0.0, '"ZNF709"': 0.0, '"VSIR"': 0.0, '"RAB6B"': 0.0, '"SYNE3"': 0.0, '"RAB40A"': 0.0, '"ZNF682"': 0.0, '"MIF"': 0.0, '"HLA-A"': 0.0, '"LDHB"': 0.0, '"CCR10"': 0.0, '"ZNF48"': 0.0, '"MADCAM1"': 0.0, '"SMOX"': 0.0, '"NME9"': 0.0, '"TATDN2P2"': 0.0, '"PIGY-DT"': 0.0, '"TUBB6"': 0.0, '"CDK5R2"': 0.0, '"MST1"': 0.0, '"SLC23A3"': 0.0, '"LRRC8A"': 0.0, '"CYP11A1"': 0.0, '"LINC00899"': 0.0, '"NMRAL2P"': 0.0, '"LINC00960"': 0.0, '"ITPR1-DT"': 0.0, '"CRB2"': 0.0, '"BFSP1"': 0.0, '"NLRX1"': 0.0, '"PLXND1"': 0.0, '"ANKRD33B"': 0.0, '"AMH"': 0.0, '"NT5M"': 0.0, '"SLC9C1"': 0.0, '"CA13"': 0.0, '"LINC02137"': 0.0, '"PERP"': 0.0, '"NKILA"': 0.0, '"RPS18P6"': 0.0, '"TMC3-AS1"': 0.0, '"SNORA28"': 0.0, '"SLC29A3"': 0.0, '"IRF1"': 0.0, '"ZNF587P1"': 0.0, '"VARS1"': 0.0, '"LINC02505"': 0.0, '"SHISA3"': 0.0, '"ASS1P12"': 0.0, '"RTL6"': 0.0, '"XBP1P1"': 0.0, '"SLC40A1"': 0.0, '"SUN3"': 0.0, '"TOB1-AS1"': 0.0, '"SERPINB9P1"': 0.0, '"GOLGA2P5"': 0.0, '"ZNF275"': 0.0, '"SMG1P7"': 0.0, '"PLK3"': 0.0, '"IKZF4"': 0.0, '"PLXNA1"': 0.0, '"SMG7"': 0.0, '"RN7SKP97"': 0.0, '"DNAJB3"': 0.0, '"LAYN"': 0.0, '"CPEB2"': 0.0, '"TP53INP1"': 0.0, '"C1QTNF1"': 0.0, '"TNFAIP8L1"': 0.0, '"ARHGAP29-AS1"': 0.0, '"AKR1B10P1"': 0.0, '"F10"': 0.0, '"EIF4A2"': 0.0, '"MRPL53P1"': 0.0, '"PLAC1"': 0.0, '"LRCOL1"': 0.0, '"MIR133A1HG"': 0.0, '"AMPD2"': 0.0, '"HYLS1"': 0.0, '"DLG2"': 0.0, '"BSPRY"': 0.0, '"H3P26"': 0.0, '"H4C5"': 0.0, '"TOB1"': 0.0, '"BTBD18"': 0.0, '"TPK1"': 0.0, '"HTRA1"': 0.0, '"CDH1"': 0.0, '"PPP1R3G"': 0.0, '"PARP3"': 0.0, '"TNPO1P1"': 0.0, '"KREMEN2"': 0.0, '"DCST1-AS1"': 0.0, '"MT-ND4L"': 0.0, '"GRN"': 0.0, '"ANK1"': 0.0, '"LINC00449"': 0.0, '"CARF"': 0.0, '"DLX2-DT"': 0.0, '"PTAFR"': 0.0, '"JADE3"': 0.0, '"LRIG3-DT"': 0.0, '"EXPH5"': 0.0, '"HTR7"': 0.0, '"ZNF470"': 0.0, '"FLI1"': 0.0, '"ZNF407"': 0.0, '"TOB2P1"': 0.0, '"EVPL"': 0.0, '"LRRC9"': 0.0, '"TNFSF15"': 0.0, '"C1orf167"': 0.0, '"ENPEP"': 0.0, '"GSTO2"': 0.0, '"BICDL1"': 0.0, '"TLE6"': 0.0, '"PAOX"': 0.0, '"TENM4"': 0.0, '"KRBA2"': 0.0, '"NCMAP"': 0.0, '"ABCA1"': 0.0, '"UBAC2-AS1"': 0.0, '"QPCT"': 0.0, '"ZIC5"': 0.0, '"HKDC1"': 0.0, '"FILIP1"': 0.0, '"TLE2"': 0.0, '"CFAP45"': 0.0, '"GUCY1B2"': 0.0, '"CD55"': 0.0, '"CFAP44"': 0.0, '"TYSND1"': 0.0, '"DSP"': 0.0, '"PKD1"': 0.0, '"CACNA1A"': 0.0, '"PDGFD"': 0.0, '"SEMA4F"': 0.0, '"GP6"': 0.0, '"CDH7"': 0.0, '"SLC25A27"': 0.0, '"VASH2"': 0.0, '"MIR374B"': 0.0, '"MIR374C"': 0.0, '"SIM1"': 0.0, '"ACACB"': 0.0, '"ADCY10P1"': 0.0, '"POLG-DT"': 0.0, '"ZGLP1"': 0.0, '"SECISBP2L"': 0.0, '"LINC02228"': 0.0, '"USP19"': 0.0, '"RDH10"': 0.0, '"VGLL1"': 0.0, '"PWAR5"': 0.0, '"ZNF230"': 0.0, '"UAP1"': 0.0, '"KDM3A"': 0.0, '"ZNF331"': 0.0, '"LINC00640"': 0.0, '"SH2B2"': 0.0, '"LINC01415"': 0.0, '"CLDN7"': 0.0, '"PAN2"': 0.0, '"POLR1A"': 0.0, '"RASGEF1B"': 0.0, '"ANKRD34B"': 0.0, '"C1orf220"': 0.0, '"MROH5"': 0.0, '"HTR1D"': 0.0, '"ZNF132"': 0.0, '"P4HB"': 0.0, '"WBP1LP2"': 0.0, '"PPP1R27"': 0.0, '"HK2-DT"': 0.0, '"AREG"': 0.0, '"SSR3"': 0.0, '"TNS2"': 0.0, '"MTMR3"': 0.0, '"CADM1"': 0.0, '"ECT2"': 0.0, '"TAGAP"': 0.0, '"H2BC3"': 0.0, '"RN7SL55P"': 0.0, '"RBCK1"': 0.0, '"P4HA2"': 0.0, '"CORO1A"': 0.0, '"CSGALNACT2-DT"': 0.0, '"ZNF672"': 0.0, '"CANX"': 0.0, '"PPRC1"': 0.0, '"PAPPA-AS1"': 0.0, '"GAS6-AS1"': 0.0, '"PLPPR3"': 0.0, '"KCTD21"': 0.0, '"ARNTL2"': 0.0, '"TAF4B"': 0.0, '"HEMK1"': 0.0, '"LRP12"': 0.0, '"ZNF345"': 0.0, '"EVC"': 0.0, '"LINC00659"': 0.0, '"LINC02096"': 0.0, '"BMP1"': 0.0, '"MKRN2OS"': 0.0, '"ODCP"': 0.0, '"H4C8"': 0.0, '"NOLC1"': 0.0, '"P2RY2"': 0.0, '"HOTTIP"': 0.0, '"VPS18"': 0.0, '"TMEM52B"': 0.0, '"LAMA4"': 0.0, '"WNT10A"': 0.0, '"POLM"': 0.0, '"LINC01275"': 0.0, '"PDLIM1P4"': 0.0, '"TMEM106A"': 0.0, '"PAUPAR"': 0.0, '"MARCHF1"': 0.0, '"MLXIPL"': 0.0, '"ZFYVE28"': 0.0, '"GPR3"': 0.0, '"CNIH3"': 0.0, '"XAF1"': 0.0, '"APLF"': 0.0, '"OPLAH"': 0.0, '"LINC01776"': 0.0, '"EOMES"': 0.0, '"SHROOM2"': 0.0, '"ST14"': 0.0, '"LINC01970"': 0.0, '"ADM2"': 0.0, '"ORC1"': 0.0, '"EHD3"': 0.0, '"C8orf58"': 0.0, '"C3orf18"': 0.0, '"HDAC5"': 0.0, '"NOL6"': 0.0, '"RPSAP70"': 0.0, '"RN7SL600P"': 0.0, '"INSYN2B"': 0.0, '"GTF2IP14"': 0.0, '"OR8G3P"': 0.0, '"P2RY1"': 0.0, '"LUZP2"': 0.0, '"FUT2"': 0.0, '"CCSER1"': 0.0, '"LINC01127"': 0.0, '"PITPNM3"': 0.0, '"LINC02378"': 0.0, '"DHDDS-AS1"': 0.0, '"ANGPTL5"': 0.0, '"BCAR1"': 0.0, '"NMB"': 0.0, '"MST1R"': 0.0, '"ZYG11A"': 0.0, '"NRG1"': 0.0, '"RBMS3"': 0.0, '"OR8B9P"': 0.0, '"NEAT1"': 0.0, '"ZDHHC23"': 0.0, '"ODAD2"': 0.0}

Apparently, the gene that is more important in determining wether a cell is under hypoxic or normoxic condition is the PGK1, which wasn't in the first genes in the other analysis.

In [ ]:
# to see the less important ones.
print({k: v for k, v in sorted(genes.items(), key=lambda item: item[1], reverse=False)})
{'"CALML5"': 0.0, '"KRT14"': 0.0, '"CCNB1"': 0.0, '"IGFBP3"': 0.0, '"KRT6A"': 0.0, '"KRT4"': 0.0, '"FN1"': 0.0, '"KRT13"': 0.0, '"KRT17"': 0.0, '"LAMC2"': 0.0, '"KIF20A"': 0.0, '"SPP1"': 0.0, '"G0S2"': 0.0, '"LRRC38"': 0.0, '"CDK1"': 0.0, '"TMPRSS4"': 0.0, '"PLK1"': 0.0, '"CDC20"': 0.0, '"AURKA"': 0.0, '"PLIN2"': 0.0, '"DHRS9"': 0.0, '"MAGEC2"': 0.0, '"UBE2C"': 0.0, '"UPK1B"': 0.0, '"CYP1B1"': 0.0, '"AKR1C1"': 0.0, '"FOS"': 0.0, '"CCNE1"': 0.0, '"TOP2A"': 0.0, '"LAMB3"': 0.0, '"LY6D"': 0.0, '"S100A14"': 0.0, '"AKR1C3"': 0.0, '"CYP1B1-AS1"': 0.0, '"TPX2"': 0.0, '"CEACAM6"': 0.0, '"ALDH1A1"': 0.0, '"FAM83D"': 0.0, '"DEPP1"': 0.0, '"SERPINB2"': 0.0, '"CCNB3"': 0.0, '"CXCL1"': 0.0, '"MUC16"': 0.0, '"VILL"': 0.0, '"KLK10"': 0.0, '"ELF3"': 0.0, '"GDF15"': 0.0, '"SERPINE1"': 0.0, '"PADI3"': 0.0, '"FAM83A"': 0.0, '"CPA4"': 0.0, '"UCA1"': 0.0, '"SCD"': 0.0, '"IGFL2-AS1"': 0.0, '"TXNIP"': 0.0, '"ZNF792"': 0.0, '"PIF1"': 0.0, '"DTL"': 0.0, '"THBS1"': 0.0, '"AMIGO1"': 0.0, '"HAS2"': 0.0, '"FST"': 0.0, '"DUSP1"': 0.0, '"GJB2"': 0.0, '"CES1"': 0.0, '"AURKB"': 0.0, '"CEACAM5"': 0.0, '"CLDN8"': 0.0, '"SLPI"': 0.0, '"VIM"': 0.0, '"FTH1"': 0.0, '"GPRC5A"': 0.0, '"MEST"': 0.0, '"HJURP"': 0.0, '"NUSAP1"': 0.0, '"CCNB2"': 0.0, '"KPNA2"': 0.0, '"PLK2"': 0.0, '"LINC01559"': 0.0, '"BEST1"': 0.0, '"TGM2"': 0.0, '"DKK1"': 0.0, '"PCSK9"': 0.0, '"KCTD11"': 0.0, '"ABCA12"': 0.0, '"CCNE2"': 0.0, '"FXYD3"': 0.0, '"CLDN4"': 0.0, '"SPRR1B"': 0.0, '"MAB21L3"': 0.0, '"GRHL3"': 0.0, '"IL1RN"': 0.0, '"C2orf16"': 0.0, '"PPFIBP2"': 0.0, '"TMEM45B"': 0.0, '"MMP10"': 0.0, '"FLNA"': 0.0, '"RASSF4"': 0.0, '"ARSI"': 0.0, '"NECTIN4"': 0.0, '"ZNF285"': 0.0, '"PIMREG"': 0.0, '"PADI2"': 0.0, '"PLAT"': 0.0, '"SDHA"': 0.0, '"EPHB6"': 0.0, '"SCEL"': 0.0, '"HEPHL1"': 0.0, '"CYP4F3"': 0.0, '"KIF23"': 0.0, '"TRIB3"': 0.0, '"TNC"': 0.0, '"KCNMA1"': 0.0, '"KRT5"': 0.0, '"SLC43A3"': 0.0, '"CCN2"': 0.0, '"SERPINB10"': 0.0, '"KRT16"': 0.0, '"SLC6A8"': 0.0, '"GPNMB"': 0.0, '"GGT6"': 0.0, '"KIF1A"': 0.0, '"CLCA2"': 0.0, '"FBLN2"': 0.0, '"KIF2C"': 0.0, '"MB"': 0.0, '"LOXL2"': 0.0, '"THY1"': 0.0, '"TRBC2"': 0.0, '"S100A9"': 0.0, '"GJB6"': 0.0, '"MOCS1"': 0.0, '"TENT5C"': 0.0, '"LVRN"': 0.0, '"KLK5"': 0.0, '"MXRA5"': 0.0, '"ABCG1"': 0.0, '"MUC20"': 0.0, '"HMGB2"': 0.0, '"VCAN"': 0.0, '"IVL"': 0.0, '"FABP4"': 0.0, '"IGF2BP1"': 0.0, '"PNMA2"': 0.0, '"TCN1"': 0.0, '"AKR1B1"': 0.0, '"LCK"': 0.0, '"KCNS1"': 0.0, '"ARL6IP1"': 0.0, '"CALHM3"': 0.0, '"CHAC1"': 0.0, '"SPOCK1"': 0.0, '"GAS6"': 0.0, '"S100P"': 0.0, '"SPTSSB"': 0.0, '"KIT"': 0.0, '"NEDD9"': 0.0, '"MYO7B"': 0.0, '"TNFSF18"': 0.0, '"KLHDC8B"': 0.0, '"CYP4F12"': 0.0, '"CFB"': 0.0, '"FBP1"': 0.0, '"AKR1B10"': 0.0, '"TCIM"': 0.0, '"NPR2"': 0.0, '"SQLE"': 0.0, '"IL22RA1"': 0.0, '"AXL"': 0.0, '"H2AC6"': 0.0, '"OASL"': 0.0, '"STC1"': 0.0, '"SPAG5"': 0.0, '"NYNRIN"': 0.0, '"DHRS2"': 0.0, '"CYP2T1P"': 0.0, '"GRAMD2A"': 0.0, '"ATP8B2"': 0.0, '"OAS1"': 0.0, '"ABCC2"': 0.0, '"TNFRSF8"': 0.0, '"CYP4F11"': 0.0, '"TMPRSS11E"': 0.0, '"ADAM8"': 0.0, '"CCDC87"': 0.0, '"MYBL2"': 0.0, '"ZMYND10"': 0.0, '"TSPAN7"': 0.0, '"ADGRL2"': 0.0, '"MFAP3L"': 0.0, '"SUSD5"': 0.0, '"SLC52A1"': 0.0, '"PLEKHB1"': 0.0, '"IL20RA"': 0.0, '"MAP1A"': 0.0, '"TIMP3"': 0.0, '"NAV2"': 0.0, '"VIPR1"': 0.0, '"RGS4"': 0.0, '"SDCBP2"': 0.0, '"CHST2"': 0.0, '"CDH6"': 0.0, '"ARNT2"': 0.0, '"NFKBIA"': 0.0, '"CSTB"': 0.0, '"PRDM1"': 0.0, '"CA12"': 0.0, '"STK4-AS1"': 0.0, '"CLDN10"': 0.0, '"CRISPLD1"': 0.0, '"COL6A2"': 0.0, '"ADAM28"': 0.0, '"GFI1"': 0.0, '"ENPP2"': 0.0, '"DISP1"': 0.0, '"ZNF229"': 0.0, '"TUBAL3"': 0.0, '"CAPN5"': 0.0, '"NELL2"': 0.0, '"ADAMTS7"': 0.0, '"NUPR1"': 0.0, '"ARL11"': 0.0, '"ADIRF"': 0.0, '"SLC7A5"': 0.0, '"AEBP1"': 0.0, '"DHX58"': 0.0, '"MAFB"': 0.0, '"CDYL2"': 0.0, '"C3"': 0.0, '"CTSD"': 0.0, '"SLC6A2"': 0.0, '"PTPRZ1"': 0.0, '"HR"': 0.0, '"MAB21L4"': 0.0, '"C1S"': 0.0, '"DLGAP5"': 0.0, '"SLC17A9"': 0.0, '"WNT9A"': 0.0, '"ITGAM"': 0.0, '"TNFRSF11B"': 0.0, '"MKI67"': 0.0, '"SUSD2"': 0.0, '"TRIM6"': 0.0, '"GNE"': 0.0, '"HHIPL1"': 0.0, '"ADIRF-AS1"': 0.0, '"SERPINB3"': 0.0, '"PLA2G4F"': 0.0, '"ANPEP"': 0.0, '"CACNA1B"': 0.0, '"L1CAM"': 0.0, '"CDCA8"': 0.0, '"DHCR7"': 0.0, '"ESX1"': 0.0, '"ADORA1"': 0.0, '"AGR2"': 0.0, '"PDE4B"': 0.0, '"GJB4"': 0.0, '"SV2A"': 0.0, '"STK32B"': 0.0, '"CXCL8"': 0.0, '"TMPRSS2"': 0.0, '"NATD1"': 0.0, '"NTRK2"': 0.0, '"HERPUD1"': 0.0, '"CCNF"': 0.0, '"MUC5AC"': 0.0, '"FBLN5"': 0.0, '"PSCA"': 0.0, '"FGFBP1"': 0.0, '"ALPP"': 0.0, '"SULT2B1"': 0.0, '"EFHD1"': 0.0, '"CDH23"': 0.0, '"CISH"': 0.0, '"KDM1A"': 0.0, '"DHRS3"': 0.0, '"ZBTB42"': 0.0, '"RNF128"': 0.0, '"LINC01018"': 0.0, '"MATN1-AS1"': 0.0, '"LTBP1"': 0.0, '"SUSD4"': 0.0, '"UBA7"': 0.0, '"F2RL2"': 0.0, '"CAPN10-DT"': 0.0, '"CCBE1"': 0.0, '"SOWAHB"': 0.0, '"SNPH"': 0.0, '"SAPCD2"': 0.0, '"SERPINB13"': 0.0, '"ATP6V0A4"': 0.0, '"FGF19"': 0.0, '"TGFB3"': 0.0, '"ZNF844"': 0.0, '"GPRC5C"': 0.0, '"GFPT2"': 0.0, '"LINC01537"': 0.0, '"ADAMTSL3"': 0.0, '"SLC24A1"': 0.0, '"ERVFRD-1"': 0.0, '"NEO1"': 0.0, '"AHNAK"': 0.0, '"SLC7A11"': 0.0, '"BOC"': 0.0, '"MYB"': 0.0, '"TRPC6"': 0.0, '"NEK2"': 0.0, '"IFIT2"': 0.0, '"PGGHG"': 0.0, '"FAM180A"': 0.0, '"PTPRO"': 0.0, '"ISM2"': 0.0, '"SCG2"': 0.0, '"KCNS3"': 0.0, '"NEFL"': 0.0, '"TENM2"': 0.0, '"ADORA2A"': 0.0, '"VEGFA"': 0.0, '"LDHA"': 0.0, '"TNFRSF19"': 0.0, '"OSBPL7"': 0.0, '"PWWP3B"': 0.0, '"ENPP1"': 0.0, '"CERS3"': 0.0, '"IDO1"': 0.0, '"ERRFI1"': 0.0, '"GLI2"': 0.0, '"PROM1"': 0.0, '"PLEKHG4"': 0.0, '"SLC39A2"': 0.0, '"ACSS2"': 0.0, '"ZNF750"': 0.0, '"SLC27A2"': 0.0, '"TJP3"': 0.0, '"GPR176"': 0.0, '"CCNA1"': 0.0, '"ALPK3"': 0.0, '"ZNF565"': 0.0, '"ZNF25"': 0.0, '"C15orf62"': 0.0, '"HSPB1"': 0.0, '"TNFAIP3"': 0.0, '"KCNH5"': 0.0, '"TMEM86A"': 0.0, '"STC2"': 0.0, '"ACTBL2"': 0.0, '"PCDH18"': 0.0, '"KRT8"': 0.0, '"TDRD12"': 0.0, '"VWA5A"': 0.0, '"KRT23"': 0.0, '"CD6"': 0.0, '"CHST4"': 0.0, '"SLC43A1"': 0.0, '"APBA1"': 0.0, '"DAPK1"': 0.0, '"REEP2"': 0.0, '"SLC14A1"': 0.0, '"LINGO3"': 0.0, '"CEACAM1"': 0.0, '"CCN1"': 0.0, '"HSPA6"': 0.0, '"PPP2R2B"': 0.0, '"CYTH4"': 0.0, '"HERC5"': 0.0, '"SLC6A14"': 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'"ITPR1-DT"': 0.0, '"CRB2"': 0.0, '"BFSP1"': 0.0, '"NLRX1"': 0.0, '"PLXND1"': 0.0, '"ANKRD33B"': 0.0, '"AMH"': 0.0, '"NT5M"': 0.0, '"SLC9C1"': 0.0, '"CA13"': 0.0, '"LINC02137"': 0.0, '"PERP"': 0.0, '"NKILA"': 0.0, '"RPS18P6"': 0.0, '"TMC3-AS1"': 0.0, '"SNORA28"': 0.0, '"SLC29A3"': 0.0, '"IRF1"': 0.0, '"ZNF587P1"': 0.0, '"VARS1"': 0.0, '"LINC02505"': 0.0, '"SHISA3"': 0.0, '"ASS1P12"': 0.0, '"RTL6"': 0.0, '"XBP1P1"': 0.0, '"SLC40A1"': 0.0, '"SUN3"': 0.0, '"TOB1-AS1"': 0.0, '"SERPINB9P1"': 0.0, '"GOLGA2P5"': 0.0, '"ZNF275"': 0.0, '"SMG1P7"': 0.0, '"PLK3"': 0.0, '"IKZF4"': 0.0, '"PLXNA1"': 0.0, '"SMG7"': 0.0, '"RN7SKP97"': 0.0, '"DNAJB3"': 0.0, '"LAYN"': 0.0, '"CPEB2"': 0.0, '"TP53INP1"': 0.0, '"C1QTNF1"': 0.0, '"TNFAIP8L1"': 0.0, '"ARHGAP29-AS1"': 0.0, '"AKR1B10P1"': 0.0, '"F10"': 0.0, '"EIF4A2"': 0.0, '"MRPL53P1"': 0.0, '"PLAC1"': 0.0, '"LRCOL1"': 0.0, '"MIR133A1HG"': 0.0, '"AMPD2"': 0.0, '"HYLS1"': 0.0, '"DLG2"': 0.0, '"BSPRY"': 0.0, '"H3P26"': 0.0, '"H4C5"': 0.0, '"TOB1"': 0.0, '"BTBD18"': 0.0, '"TPK1"': 0.0, '"HTRA1"': 0.0, '"CDH1"': 0.0, '"PPP1R3G"': 0.0, '"PARP3"': 0.0, '"TNPO1P1"': 0.0, '"KREMEN2"': 0.0, '"DCST1-AS1"': 0.0, '"MT-ND4L"': 0.0, '"GRN"': 0.0, '"ANK1"': 0.0, '"LINC00449"': 0.0, '"CARF"': 0.0, '"DLX2-DT"': 0.0, '"PTAFR"': 0.0, '"JADE3"': 0.0, '"LRIG3-DT"': 0.0, '"EXPH5"': 0.0, '"HTR7"': 0.0, '"ZNF470"': 0.0, '"FLI1"': 0.0, '"ZNF407"': 0.0, '"TOB2P1"': 0.0, '"EVPL"': 0.0, '"LRRC9"': 0.0, '"TNFSF15"': 0.0, '"C1orf167"': 0.0, '"ENPEP"': 0.0, '"GSTO2"': 0.0, '"BICDL1"': 0.0, '"TLE6"': 0.0, '"PAOX"': 0.0, '"TENM4"': 0.0, '"KRBA2"': 0.0, '"NCMAP"': 0.0, '"ABCA1"': 0.0, '"UBAC2-AS1"': 0.0, '"QPCT"': 0.0, '"ZIC5"': 0.0, '"HKDC1"': 0.0, '"FILIP1"': 0.0, '"TLE2"': 0.0, '"CFAP45"': 0.0, '"GUCY1B2"': 0.0, '"CD55"': 0.0, '"CFAP44"': 0.0, '"TYSND1"': 0.0, '"DSP"': 0.0, '"PKD1"': 0.0, '"CACNA1A"': 0.0, '"PDGFD"': 0.0, '"SEMA4F"': 0.0, '"GP6"': 0.0, '"CDH7"': 0.0, '"SLC25A27"': 0.0, '"VASH2"': 0.0, '"MIR374B"': 0.0, '"MIR374C"': 0.0, '"SIM1"': 0.0, '"ACACB"': 0.0, '"ADCY10P1"': 0.0, '"POLG-DT"': 0.0, '"ZGLP1"': 0.0, '"SECISBP2L"': 0.0, '"LINC02228"': 0.0, '"USP19"': 0.0, '"RDH10"': 0.0, '"VGLL1"': 0.0, '"PWAR5"': 0.0, '"ZNF230"': 0.0, '"UAP1"': 0.0, '"KDM3A"': 0.0, '"ZNF331"': 0.0, '"LINC00640"': 0.0, '"SH2B2"': 0.0, '"LINC01415"': 0.0, '"CLDN7"': 0.0, '"PAN2"': 0.0, '"POLR1A"': 0.0, '"RASGEF1B"': 0.0, '"ANKRD34B"': 0.0, '"C1orf220"': 0.0, '"MROH5"': 0.0, '"HTR1D"': 0.0, '"ZNF132"': 0.0, '"P4HB"': 0.0, '"WBP1LP2"': 0.0, '"PPP1R27"': 0.0, '"HK2-DT"': 0.0, '"AREG"': 0.0, '"SSR3"': 0.0, '"TNS2"': 0.0, '"MTMR3"': 0.0, '"CADM1"': 0.0, '"ECT2"': 0.0, '"TAGAP"': 0.0, '"H2BC3"': 0.0, '"RN7SL55P"': 0.0, '"RBCK1"': 0.0, '"P4HA2"': 0.0, '"CORO1A"': 0.0, '"CSGALNACT2-DT"': 0.0, '"ZNF672"': 0.0, '"CANX"': 0.0, '"PPRC1"': 0.0, '"PAPPA-AS1"': 0.0, '"GAS6-AS1"': 0.0, '"PLPPR3"': 0.0, '"KCTD21"': 0.0, '"ARNTL2"': 0.0, '"TAF4B"': 0.0, '"HEMK1"': 0.0, '"LRP12"': 0.0, '"ZNF345"': 0.0, '"EVC"': 0.0, '"LINC00659"': 0.0, '"LINC02096"': 0.0, '"BMP1"': 0.0, '"MKRN2OS"': 0.0, '"ODCP"': 0.0, '"H4C8"': 0.0, '"NOLC1"': 0.0, '"P2RY2"': 0.0, '"HOTTIP"': 0.0, '"VPS18"': 0.0, '"TMEM52B"': 0.0, '"LAMA4"': 0.0, '"WNT10A"': 0.0, '"POLM"': 0.0, '"LINC01275"': 0.0, '"PDLIM1P4"': 0.0, '"TMEM106A"': 0.0, '"PAUPAR"': 0.0, '"MARCHF1"': 0.0, '"MLXIPL"': 0.0, '"ZFYVE28"': 0.0, '"GPR3"': 0.0, '"CNIH3"': 0.0, '"XAF1"': 0.0, '"APLF"': 0.0, '"OPLAH"': 0.0, '"LINC01776"': 0.0, '"EOMES"': 0.0, '"SHROOM2"': 0.0, '"ST14"': 0.0, '"LINC01970"': 0.0, '"ADM2"': 0.0, '"ORC1"': 0.0, '"EHD3"': 0.0, '"C8orf58"': 0.0, '"C3orf18"': 0.0, '"HDAC5"': 0.0, '"NOL6"': 0.0, '"RPSAP70"': 0.0, '"RN7SL600P"': 0.0, '"INSYN2B"': 0.0, '"GTF2IP14"': 0.0, '"OR8G3P"': 0.0, '"P2RY1"': 0.0, '"LUZP2"': 0.0, '"FUT2"': 0.0, '"CCSER1"': 0.0, '"LINC01127"': 0.0, '"PITPNM3"': 0.0, '"LINC02378"': 0.0, '"DHDDS-AS1"': 0.0, '"ANGPTL5"': 0.0, '"BCAR1"': 0.0, '"NMB"': 0.0, '"MST1R"': 0.0, '"ZYG11A"': 0.0, '"NRG1"': 0.0, '"RBMS3"': 0.0, '"OR8B9P"': 0.0, '"NEAT1"': 0.0, '"ZDHHC23"': 0.0, '"ODAD2"': 0.0, '"MAGED1"': 0.0001846118997281788, '"SNAI2"': 0.0002079506021637069, '"AOC2"': 0.00024230157913393362, '"ELFN1"': 0.000242340409515206, '"UCP2"': 0.0002423404095152063, '"SH3BP5L"': 0.00024237828112163147, '"PLA2G4A"': 0.0002423782811216315, '"TNFRSF9"': 0.00024241340361445783, '"GPT2"': 0.0002424152290303395, '"HCP5"': 0.00024241522903033954, '"GLIPR2"': 0.0002424512866279943, '"CDKN1A"': 0.00024248079627826405, '"SCIN"': 0.00024248079627826468, '"FAM13A"': 0.00024252431412396657, '"MIF-AS1"': 0.00024255952380952382, '"BLNK"': 0.0002425974296579081, '"SRXN1"': 0.0002428672103090708, '"TBX5-AS1"': 0.0002428672103090708, '"COX6B2"': 0.00024289011248614372, '"LINC02561"': 0.00024289011248614372, '"SERPINB5"': 0.00024292537527831624, '"WTAPP1"': 0.00024295245678513576, '"PCSK5"': 0.00024314446958208048, '"AKR1C2"': 0.00024319010480534982, '"IL1A"': 0.00024321885202283872, '"H4C3"': 0.00024325332670065906, '"SLC6A17"': 0.00024328699964178634, '"SPATA18"': 0.0002433198984923121, '"TDRD7"': 0.00024358655043586552, '"RRM2"': 0.0002436549473121457, '"H3C6"': 0.00024367676767676622, '"LHX4"': 0.00024405725950669608, '"PXN"': 0.00024413096482062003, '"MT1X"': 0.00024413096482062003, '"CRY2"': 0.0002441632231404959, '"PFKFB4"': 0.0002446030827277209, '"PEX5"': 0.0002446499191946693, '"KRT18"': 0.00024598372912979795, '"SLC16A2"': 0.00024607487922705313, '"HSPA5"': 0.0002460748792270532, '"SLFN5"': 0.0002467985168536302, '"TPPP"': 0.000250566539226333, '"SFN"': 0.0004783902972644367, '"ISG15"': 0.000478545618789522, '"ID3"': 0.0004786897590361453, '"SH3TC2-DT"': 0.00047869710521522216, '"KYNU"': 0.00047882283822037056, '"BRD2"': 0.0004788412910902879, '"BCL6"': 0.0004788448968500537, '"NQO1"': 0.00047884489685005383, '"DEGS2"': 0.00047909656959430676, '"FAM47E"': 0.0004792561620558642, '"ALOXE3"': 0.00047956313327018657, '"CASTOR2"': 0.0004797007410559159, '"PLAC8"': 0.0004797007410559169, '"ANXA3"': 0.0004797007410559169, '"MMP1"': 0.00048013485937361373, '"PPP1R3B"': 0.00048023664176114194, '"HBP1"': 0.0004807676767676759, '"SLC2A12"': 0.00048094098883572425, '"C14orf132"': 0.00048094098883572425, '"PLOD2"': 0.0004811097992916174, '"ZNF333"': 0.00048161128027511215, '"KRT19"': 0.0004822175059489343, '"IMPDH1P10"': 0.0004824524312896407, '"LAMA3"': 0.000482584465343086, '"ADAMTS1"': 0.0004827134986225896, '"LAMP3"': 0.0004848219753302423, '"IL1RAPL1"': 0.00048559111690796503, '"SLC7A8"': 0.0004882318485582683, '"EHF"': 0.0004884626910398547, '"RAET1L"': 0.0004898817872169915, '"ALDOA"': 0.0004937850860999877, '"EGR1"': 0.0004987165737511152, '"GPX2"': 0.0007092563291139227, '"MCM4"': 0.0007095480840827079, '"ALDOC"': 0.0007096135218380296, '"EGLN1"': 0.0007098272608506315, '"THEMIS2"': 0.00070993031358885, '"LINC02693"': 0.0007102396514161218, '"SLC2A1"': 0.0007104052850299528, '"VCPIP1"': 0.0007107558139534864, '"NRCAM"': 0.0007114797031863813, '"LINC02709"': 0.0007116626794258369, '"NRP1"': 0.0007131754758898458, '"GLRX"': 0.0007137656691849914, '"BTG2"': 0.0007162121212121224, '"GLRA3"': 0.0007164835164835161, '"FYB1"': 0.0007164835164835165, '"CEMIP2"': 0.00071800656070319, '"PSAP"': 0.0007194132537158435, '"LRRC37A15P"': 0.0007200218383958704, '"SQSTM1"': 0.0007244730656025917, '"IL24"': 0.0007269818213811973, '"PIP5K1A"': 0.0007276785714285704, '"TXNRD1"': 0.0007278059061337649, '"LAMC1"': 0.0007303711840888068, '"MRNIP"': 0.0009116615405572046, '"TMSB4X"': 0.0009351692484222606, '"ANTXR2"': 0.0009376688063418569, '"SVEP1"': 0.0009378596087456847, '"ZNF416"': 0.0009408369408369409, '"SYTL3"': 0.0009408369408369415, '"DCLK1"': 0.0009492422738402486, '"SLCO4A1"': 0.0009552692573341235, '"RNASE7"': 0.0009555804259806406, '"SLC2A3"': 0.0009576672468065446, '"ZNF143"': 0.0009582549246039886, '"PLAU"': 0.0009690943944272136, '"FTL"': 0.0011852123210050725, '"CDK2AP2"': 0.0011932703760057328, '"IL17RD"': 0.0014321312523344835, '"MUC1"': 0.001434924295836034, '"CD44"': 0.001577551533433888, '"KLHL24"': 0.0016755120577069164, '"F3"': 0.0016865150616515079, '"ZFYVE1"': 0.0018494232625559577, '"FAM162A"': 0.00190783790465825, '"PPIF"': 0.001925520722112464, '"ENO2"': 0.001985921212941655, '"UGT1A6"': 0.0020905611731218375, '"KDM5B"': 0.00212678801708075, '"PFKFB3"': 0.002129661023551652, '"INSIG1"': 0.002550127433425332, '"BHLHE40"': 0.009046375862947207, '"ERO1A"': 0.009754628932711123, '"FUT11"': 0.017783749905413676, '"BNIP3L"': 0.018178378198055508, '"CA9"': 0.019256528360955545, '"ANGPTL4"': 0.03573394372296992, '"BNIP3"': 0.03737047723028583, '"EGLN3"': 0.05617846108839006, '"NDRG1"': 0.09159165949503784, '"DDIT4"': 0.21375320859702115, '"PGK1"': 0.41121140437726483}

To see the differences in distribution of the gene, we plot some boxplots.

In [ ]:
Gene_Hypo = HCC1806_Hypo_f_n_trans['"PGK1"']
Gene_Hypo
Out[ ]:
"output.STAR.PCRPlate1G1_Hypoxia_S102_Aligned.sortedByCoord.out.bam"    6180
"output.STAR.PCRPlate1G2_Hypoxia_S2_Aligned.sortedByCoord.out.bam"      5433
"output.STAR.PCRPlate1G3_Hypoxia_S7_Aligned.sortedByCoord.out.bam"      4159
"output.STAR.PCRPlate1G4_Hypoxia_S107_Aligned.sortedByCoord.out.bam"    6056
"output.STAR.PCRPlate1H1_Hypoxia_S103_Aligned.sortedByCoord.out.bam"    6424
                                                                        ... 
"output.STAR.PCRPlate4F5_Hypoxia_S229_Aligned.sortedByCoord.out.bam"    4237
"output.STAR.PCRPlate4G1_Hypoxia_S193_Aligned.sortedByCoord.out.bam"    5388
"output.STAR.PCRPlate4G2_Hypoxia_S198_Aligned.sortedByCoord.out.bam"    5883
"output.STAR.PCRPlate4G6_Hypoxia_S232_Aligned.sortedByCoord.out.bam"    6607
"output.STAR.PCRPlate4H2_Hypoxia_S199_Aligned.sortedByCoord.out.bam"    4274
Name: "PGK1", Length: 97, dtype: int64
In [ ]:
Gene_Norm = HCC1806_Norm_f_n_trans['"PGK1"']
Gene_Norm
Out[ ]:
"output.STAR.PCRPlate1G12_Normoxia_S32_Aligned.sortedByCoord.out.bam"     1125
"output.STAR.PCRPlate1G7_Normoxia_S118_Aligned.sortedByCoord.out.bam"     1159
"output.STAR.PCRPlate1G8_Normoxia_S19_Aligned.sortedByCoord.out.bam"      2600
"output.STAR.PCRPlate1G9_Normoxia_S121_Aligned.sortedByCoord.out.bam"     1321
"output.STAR.PCRPlate1H9_Normoxia_S122_Aligned.sortedByCoord.out.bam"     1448
                                                                          ... 
"output.STAR.PCRPlate4G7_Normoxia_S204_Aligned.sortedByCoord.out.bam"     1607
"output.STAR.PCRPlate4H10_Normoxia_S210_Aligned.sortedByCoord.out.bam"    1259
"output.STAR.PCRPlate4H11_Normoxia_S214_Aligned.sortedByCoord.out.bam"    1145
"output.STAR.PCRPlate4H7_Normoxia_S205_Aligned.sortedByCoord.out.bam"     1191
"output.STAR.PCRPlate4H9_Normoxia_S236_Aligned.sortedByCoord.out.bam"     1995
Name: "PGK1", Length: 85, dtype: int64
In [ ]:
Gene_Hypo.describe()
Out[ ]:
count      97.000000
mean     5289.773196
std      1559.183330
min         0.000000
25%      4237.000000
50%      5264.000000
75%      6318.000000
max      8370.000000
Name: "PGK1", dtype: float64
In [ ]:
Gene_Norm.describe()
Out[ ]:
count      85.000000
mean     1430.070588
std       476.128229
min         0.000000
25%      1159.000000
50%      1409.000000
75%      1658.000000
max      3737.000000
Name: "PGK1", dtype: float64
In [ ]:
plt.figure(figsize=(16,16))
sns.boxplot(data=[Gene_Norm, Gene_Hypo])
plt.xticks(ticks = [0, 1], labels=["Normoxic", "Hypoxic"])
plt.title("PGK1")
plt.show()

We can see from the plot that the gene PGK1 has very different distribution between the hypoxic and the normoxic cells.

We now plot the gene CA9 because it was the one that, from the previous analysis, seemed more important.

In [ ]:
Gene_Hypo = HCC1806_Hypo_f_n_trans['"CA9"']
Gene_Hypo
Out[ ]:
"output.STAR.PCRPlate1G1_Hypoxia_S102_Aligned.sortedByCoord.out.bam"    977
"output.STAR.PCRPlate1G2_Hypoxia_S2_Aligned.sortedByCoord.out.bam"      155
"output.STAR.PCRPlate1G3_Hypoxia_S7_Aligned.sortedByCoord.out.bam"      437
"output.STAR.PCRPlate1G4_Hypoxia_S107_Aligned.sortedByCoord.out.bam"    257
"output.STAR.PCRPlate1H1_Hypoxia_S103_Aligned.sortedByCoord.out.bam"    309
                                                                       ... 
"output.STAR.PCRPlate4F5_Hypoxia_S229_Aligned.sortedByCoord.out.bam"    219
"output.STAR.PCRPlate4G1_Hypoxia_S193_Aligned.sortedByCoord.out.bam"    261
"output.STAR.PCRPlate4G2_Hypoxia_S198_Aligned.sortedByCoord.out.bam"     82
"output.STAR.PCRPlate4G6_Hypoxia_S232_Aligned.sortedByCoord.out.bam"    804
"output.STAR.PCRPlate4H2_Hypoxia_S199_Aligned.sortedByCoord.out.bam"     61
Name: "CA9", Length: 97, dtype: int64
In [ ]:
Gene_Norm = HCC1806_Norm_f_n_trans['"CA9"']
Gene_Norm
Out[ ]:
"output.STAR.PCRPlate1G12_Normoxia_S32_Aligned.sortedByCoord.out.bam"     0
"output.STAR.PCRPlate1G7_Normoxia_S118_Aligned.sortedByCoord.out.bam"     0
"output.STAR.PCRPlate1G8_Normoxia_S19_Aligned.sortedByCoord.out.bam"      0
"output.STAR.PCRPlate1G9_Normoxia_S121_Aligned.sortedByCoord.out.bam"     0
"output.STAR.PCRPlate1H9_Normoxia_S122_Aligned.sortedByCoord.out.bam"     0
                                                                         ..
"output.STAR.PCRPlate4G7_Normoxia_S204_Aligned.sortedByCoord.out.bam"     1
"output.STAR.PCRPlate4H10_Normoxia_S210_Aligned.sortedByCoord.out.bam"    0
"output.STAR.PCRPlate4H11_Normoxia_S214_Aligned.sortedByCoord.out.bam"    0
"output.STAR.PCRPlate4H7_Normoxia_S205_Aligned.sortedByCoord.out.bam"     0
"output.STAR.PCRPlate4H9_Normoxia_S236_Aligned.sortedByCoord.out.bam"     0
Name: "CA9", Length: 85, dtype: int64
In [ ]:
Gene_Hypo.describe()
Out[ ]:
count      97.000000
mean      349.525773
std       323.676346
min         0.000000
25%       115.000000
50%       263.000000
75%       500.000000
max      1779.000000
Name: "CA9", dtype: float64
In [ ]:
Gene_Norm.describe()
Out[ ]:
count    85.000000
mean      3.094118
std      10.444437
min       0.000000
25%       0.000000
50%       0.000000
75%       0.000000
max      71.000000
Name: "CA9", dtype: float64
In [ ]:
plt.figure(figsize=(16,16))
sns.boxplot(data=[Gene_Norm, Gene_Hypo])
plt.xticks(ticks = [0, 1], labels=["Normoxic", "Hypoxic"])
plt.title("CA9")
plt.show()

Again, we can see that the distribution of the genes under hypoxic and normoxic condition are very much different.\ But it is quite nice to see that we didn't need to use any ylim. We can interpret this by saying that, in HCC1806, the outliners have less important meaning in finding wether a cell is hypoxic or normoxic than in MCF7.

Clustering Data

To better visualize the data, we performed a PCA in 2 dimensions and then used the data for K-means clustering. In such a way, we are trying to split the data in two groups and, by using different colours for hypoxic and normoxic cells, check whether the clustering assigned them correctly.

In [ ]:
from sklearn.decomposition import PCA
In [ ]:
from sklearn.cluster import KMeans
In [ ]:
def plot_data_C(X, col):
  for i in range(len(X)):
    plt.plot(X[i][0], X[i][1], 'k.', markersize=2, c=col[i])

def plot_centroids_C(centroids, weights=None, circle_color='w', cross_color='k'):
    if weights is not None:
        centroids = centroids[weights > weights.max() / 10]
    plt.scatter(centroids[:, 0], centroids[:, 1],
                marker='o', s=35, linewidths=8,
                color=circle_color, zorder=10, alpha=0.9)
    plt.scatter(centroids[:, 0], centroids[:, 1],
                marker='x', s=2, linewidths=12,
                color=cross_color, zorder=11, alpha=1)

def plot_decision_boundaries(clusterer, X, col, resolution=1000, show_centroids=True,
                             show_xlabels=True, show_ylabels=True):
    mins = X.min(axis=0) - 0.1
    maxs = X.max(axis=0) + 0.1
    xx, yy = np.meshgrid(np.linspace(mins[0], maxs[0], resolution),
                         np.linspace(mins[1], maxs[1], resolution))
    Z = clusterer.predict(np.c_[xx.ravel(), yy.ravel()])
    Z = Z.reshape(xx.shape)

    plt.contourf(Z, extent=(mins[0], maxs[0], mins[1], maxs[1]),
                cmap="Pastel2")
    plt.contour(Z, extent=(mins[0], maxs[0], mins[1], maxs[1]),
                linewidths=1, colors='k')
    plot_data_C(X, col)
    if show_centroids:
        plot_centroids_C(clusterer.cluster_centers_)

    if show_xlabels:
        plt.xlabel("$x_1$", fontsize=14)
    else:
        plt.tick_params(labelbottom=False)
    if show_ylabels:
        plt.ylabel("$x_2$", fontsize=14, rotation=0)
    else:
        plt.tick_params(labelleft=False)
In [ ]:
pcaM = PCA(n_components = 2)
HCC1806_lowT = pcaM.fit_transform(HCC1806_f_n.T)
HCC1806_ret = pcaM.inverse_transform(HCC1806_lowT)
print(HCC1806_lowT.shape)
(182, 2)
In [ ]:
col = []
for c in HCC1806_f_n.columns:
  if "Hypo" in c:
    col.append("r")
  else:
    col.append("b")
print(len(col))
182
In [ ]:
index = HCC1806_f_n.T.index
HCC1806_hyponormo = np.zeros((len(index)), dtype = 'int64')
for i in range(len(index)):
    HCC1806_hyponormo[i] = not 'Hypo' in index[i] # 0 Hypo 1 Norm

print(HCC1806_hyponormo)
[1 0 0 0 0 1 1 1 0 0 0 0 1 1 0 0 0 0 1 1 1 0 0 0 0 0 1 1 1 1 0 0 0 0 0 1 1
 1 0 0 0 0 1 1 1 0 0 0 0 1 1 1 1 0 0 0 0 0 1 1 1 0 0 1 1 1 1 1 0 0 0 0 1 1
 1 0 0 0 0 1 1 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 1 1 0 0 1 1 1 0 0 0 0 0 1 1 1
 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 1 0 0 1 1 1 1 1 1 0 0 0 1
 1 1 1 0 0 0 0 1 1 1 1 0 0 0 1 1 1 0 0 0 0 1 1 1 1 0 0 0 1 1 1 0 1 1]
In [ ]:
from sklearn import metrics
k = 2
for i in [42, 44, 28, 36, 40]:
  kmeans = KMeans(n_clusters=k, random_state=i)
  y_pred = kmeans.fit_predict(HCC1806_lowT)
  mapping = {}
  for class_id in np.unique(HCC1806_hyponormo):
      mode, _ = stats.mode(y_pred[HCC1806_hyponormo==class_id]) # look at all samples with a given label and study what is the most common label given by the Gaussian mixture
      mapping[mode[0]] = class_id
  # print([mapping[cluster_id] for cluster_id in y_pred if cluster_id in mapping.keys else val = 1 - val])
  # y_pred = np.array([mapping[cluster_id] for cluster_id in y_pred])
  # print(accuracy_score(y_pred, MCF7_hyponormo))
  print("fraction of correct predictions", np.sum(y_pred==HCC1806_hyponormo) / len(y_pred))
  plt.figure(figsize=(8, 4))
  plot_decision_boundaries(kmeans, HCC1806_lowT, col)
  plt.show()
fraction of correct predictions 0.5164835164835165
fraction of correct predictions 0.5164835164835165
fraction of correct predictions 0.5164835164835165
fraction of correct predictions 0.5164835164835165
fraction of correct predictions 0.5164835164835165

We tried to use different random states to calculate an average score of our K-means clustering. We can see that it predicts correctly only around 48% of the data in every case, this is probably due to the fact that a PCA in 2 dimention retain low variance in this particular dataset.

Let's now try clustering without applying PCA.

In [ ]:
from sklearn import metrics
k = 2
accuracy_scores = []
for i in [42, 52, 28, 37, 67]:
  kmeans = KMeans(n_clusters=k, random_state=i)
  y_pred = kmeans.fit_predict(HCC1806_f_n.T)

  mapping = {}
  for class_id in np.unique(HCC1806_hyponormo):
      mode, _ = stats.mode(y_pred[HCC1806_hyponormo==class_id]) # look at all samples with a given label and study what is the most common label given by the Gaussian mixture
      mapping[mode[0]] = class_id
  # y_pred = np.array([mapping[cluster_id] for cluster_id in y_pred])
  print(accuracy_score(HCC1806_hyponormo, y_pred))
  print("fraction of correct predictions", np.sum(y_pred==HCC1806_hyponormo) / len(y_pred))
  accuracy_scores.append(accuracy_score(HCC1806_hyponormo, y_pred))
0.5164835164835165
fraction of correct predictions 0.5164835164835165
0.4835164835164835
fraction of correct predictions 0.4835164835164835
0.47802197802197804
fraction of correct predictions 0.47802197802197804
0.5164835164835165
fraction of correct predictions 0.5164835164835165
0.4835164835164835
fraction of correct predictions 0.4835164835164835
In [ ]:
print("Average accuracy score:", sum(accuracy_scores)/len(accuracy_scores))
Average accuracy score: 0.4956043956043956

We then repeated the clustering using the dataset not processed by the PCA, obtaining a slightly higher accuracy score. Even using the whole dataset, the clustering accuracy is still pretty low.

In [ ]:
from sklearn.cluster import kmeans_plusplus

k = 2
accuracy_scores = []
for i in [110, 42, 66, 80, 120]:
  centroids, indices = kmeans_plusplus(HCC1806_f_n.T.to_numpy(), n_clusters = 2, random_state=i)
  kmeans = KMeans(n_clusters=k, random_state=i)
  kmeans.fit(centroids)
  y_pred = kmeans.predict(HCC1806_f_n.T)

  mapping = {}
  for class_id in np.unique(HCC1806_hyponormo):
      mode, _ = stats.mode(y_pred[HCC1806_hyponormo==class_id]) # look at all samples with a given label and study what is the most common label given by the Gaussian mixture
      mapping[mode[0]] = class_id
  y_pred = np.array([mapping[cluster_id] for cluster_id in y_pred])
  print(accuracy_score(HCC1806_hyponormo, y_pred))
  #print("fraction of correct predictions", np.sum(y_pred==MCF7_hyponormo) / len(y_pred))
  accuracy_scores.append(accuracy_score(HCC1806_hyponormo, y_pred))
print("Average accuracy score:", sum(accuracy_scores)/len(accuracy_scores))
0.6758241758241759
0.9120879120879121
0.7967032967032966
0.7747252747252747
0.7582417582417582
Average accuracy score: 0.7835164835164835

We finally tried to find the centroids using K-means++ and then used them to cluster the data. We can see that the result is much better than the previous case where we used K-means.

DROP SEQ EXPERIMENT

MCF7

Understanding the data
In [ ]:
MCF7_drop_f_n.describe()
Out[ ]:
"AAAAACCTATCG_Normoxia" "AAAACAACCCTA_Normoxia" "AAAACACTCTCA_Normoxia" "AAAACCAGGCAC_Normoxia" "AAAACCTAGCTC_Normoxia" "AAAACCTCCGGG_Normoxia" "AAAACTCGTTGC_Normoxia" "AAAAGAGCTCTC_Normoxia" "AAAAGCTAGGCG_Normoxia" "AAAATCGCATTT_Normoxia" ... "TTTTACAGGATC_Hypoxia" "TTTTACCACGTA_Hypoxia" "TTTTATGCTACG_Hypoxia" "TTTTCCAGACGC_Hypoxia" "TTTTCGCGCTCG_Hypoxia" "TTTTCGCGTAGA_Hypoxia" "TTTTCGTCCGCT_Hypoxia" "TTTTCTCCGGCT_Hypoxia" "TTTTGTTCAAAG_Hypoxia" "TTTTTTGTATGT_Hypoxia"
count 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 ... 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000
mean 0.034000 0.030333 0.027000 0.032333 0.045333 0.047333 0.030000 0.027333 0.032000 0.027333 ... 0.052333 0.043667 0.033667 0.033000 0.025333 0.037000 0.046333 0.055667 0.038000 0.033000
std 0.277254 0.220823 0.195662 0.233751 0.246235 0.299649 0.204403 0.292030 0.281074 0.237918 ... 0.364654 0.244499 0.340449 0.302117 0.208261 0.286924 0.301469 0.358623 0.240642 0.244808
min 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
25% 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
50% 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
75% 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
max 4.000000 4.000000 5.000000 6.000000 4.000000 8.000000 6.000000 13.000000 7.000000 6.000000 ... 7.000000 4.000000 10.000000 8.000000 6.000000 7.000000 7.000000 9.000000 6.000000 6.000000

8 rows × 21626 columns

From the data we can immediately notice that the mean of genes expressed and the maximum value is much lower compared to the data obtained using SmartSeq

Hypo vs Norm

Now we will analize the difference between the hypoxic and normoxic cells of a particular gene.

In [ ]:
MCF7_drop_Hypo_f_n = MCF7_drop_f_n.loc[:, MCF7_drop_f_n.columns.str.contains('Hypoxia')]
MCF7_drop_Hypo_f_n
Out[ ]:
"AAAAAATCCGGC_Hypoxia" "AAAAACACGATC_Hypoxia" "AAAAATGGGGGA_Hypoxia" "AAAACATCTTGC_Hypoxia" "AAAACCAGCCCA_Hypoxia" "AAAACCTGAGTT_Hypoxia" "AAAACCTTCAAG_Hypoxia" "AAAACGATATTC_Hypoxia" "AAAACGCGCTGG_Hypoxia" "AAAAGCAATTGA_Hypoxia" ... "TTTTACAGGATC_Hypoxia" "TTTTACCACGTA_Hypoxia" "TTTTATGCTACG_Hypoxia" "TTTTCCAGACGC_Hypoxia" "TTTTCGCGCTCG_Hypoxia" "TTTTCGCGTAGA_Hypoxia" "TTTTCGTCCGCT_Hypoxia" "TTTTCTCCGGCT_Hypoxia" "TTTTGTTCAAAG_Hypoxia" "TTTTTTGTATGT_Hypoxia"
"MALAT1" 0 0 0 2 0 0 7 2 0 3 ... 0 2 1 0 1 0 1 0 0 4
"MT-RNR2" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"NEAT1" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"H1-5" 0 0 0 0 1 0 0 1 0 0 ... 0 1 0 0 1 0 0 1 0 0
"TFF1" 9 1 1 1 4 0 3 9 4 0 ... 2 3 8 0 0 3 4 2 6 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
"BRWD1-AS2" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"RPS19BP1" 0 0 0 1 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"AUNIP" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"TNK2" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"SUDS3" 0 1 0 0 0 0 0 0 0 1 ... 0 0 0 0 0 0 0 1 0 0

3000 rows × 8921 columns

In [ ]:
MCF7_drop_Norm_f_n = MCF7_drop_f_n.loc[:, MCF7_drop_f_n.columns.str.contains('Normoxia')]
MCF7_drop_Norm_f_n
Out[ ]:
"AAAAACCTATCG_Normoxia" "AAAACAACCCTA_Normoxia" "AAAACACTCTCA_Normoxia" "AAAACCAGGCAC_Normoxia" "AAAACCTAGCTC_Normoxia" "AAAACCTCCGGG_Normoxia" "AAAACTCGTTGC_Normoxia" "AAAAGAGCTCTC_Normoxia" "AAAAGCTAGGCG_Normoxia" "AAAATCGCATTT_Normoxia" ... "TTTTGCGGAATG_Normoxia" "TTTTGGTTTTGG_Normoxia" "TTTTGTAGGTTG_Normoxia" "TTTTGTCGATTT_Normoxia" "TTTTTACCCTAA_Normoxia" "TTTTTACCTCCC_Normoxia" "TTTTTCGAATCA_Normoxia" "TTTTTCGACCAC_Normoxia" "TTTTTGCGCCAT_Normoxia" "TTTTTTGTCATA_Normoxia"
"MALAT1" 1 3 3 6 4 5 1 13 3 3 ... 1 4 0 8 16 0 2 1 1 5
"MT-RNR2" 0 0 0 2 0 0 2 1 7 0 ... 0 2 11 2 5 1 1 1 0 1
"NEAT1" 0 0 0 0 0 2 0 1 2 0 ... 0 0 0 0 0 1 0 0 0 0
"H1-5" 0 0 0 0 0 2 0 0 0 0 ... 1 0 1 0 0 1 1 0 0 0
"TFF1" 4 1 1 1 0 0 0 2 0 1 ... 0 0 1 2 0 0 2 4 4 1
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
"BRWD1-AS2" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"RPS19BP1" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"AUNIP" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"TNK2" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"SUDS3" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0

3000 rows × 12705 columns

In [ ]:
MCF7_drop_Hypo_f_n_trans = MCF7_drop_Hypo_f_n.T
MCF7_drop_Norm_f_n_trans = MCF7_drop_Norm_f_n.T
In [ ]:
MCF7_drop_Hypo_f_n_trans_d = MCF7_drop_Hypo_f_n.T.describe()
MCF7_drop_Norm_f_n_trans_d = MCF7_drop_Norm_f_n.T.describe()
In [ ]:
MCF7_drop_f_n_logratio = np.log2(MCF7_drop_Hypo_f_n_trans_d.iloc[1] + 1) - np.log2(MCF7_drop_Norm_f_n_trans_d.iloc[1] + 1)
MCF7_drop_f_n_logratio.sort_values(ascending=False)
Out[ ]:
"TFF1"       1.294372
"RPS19"      0.933220
"TMSB10"     0.903335
"RPL13"      0.857870
"RPS14"      0.820595
               ...   
"TOB1"      -0.341241
"SET"       -0.409687
"MT-RNR1"   -0.550049
"MALAT1"    -0.714097
"MT-RNR2"   -1.116191
Name: mean, Length: 3000, dtype: float64

Apparently, the gene TFF1 is the most important in the MCF7 dropseq dataset.

Check with random forest which cells have higher importance

We now try to get the most important genes with a random forest to check wheter they are the same as the ones we found before.

In [ ]:
data_test = MCF7_drop_f_n
In [ ]:
# Let's load the packages
import numpy as np
import pandas as pd
from sklearn.datasets import load_boston
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestRegressor
from sklearn.inspection import permutation_importance
#import shap
from matplotlib import pyplot as plt

plt.rcParams.update({'figure.figsize': (12.0, 8.0)})
plt.rcParams.update({'font.size': 14})
In [ ]:
index = data_test.T.index
y = np.zeros((len(index)),dtype = 'int64')
for i in range(len(index)):
    y[i] = not 'Hypo' in index[i] # 0 Hypo 1 Norm
In [ ]:
X_train, X_test, y_train, y_test = train_test_split(data_test.T, y, test_size= 0.1, random_state= 42)
In [ ]:
rf = RandomForestRegressor(n_estimators=10)
rf.fit(X_train, y_train)
Out[ ]:
RandomForestRegressor(n_estimators=10)
In [ ]:
genes_importance = rf.feature_importances_
In [ ]:
genes = {}
for n, g in zip(data_test.index, genes_importance):
  genes[n] = g
print({k: v for k, v in sorted(genes.items(), key=lambda item: item[1], reverse=True)})
{'"TFF1"': 0.28485557430418823, '"MT-RNR2"': 0.11641265860620124, '"GAPDH"': 0.08547181749177711, '"PGK1"': 0.06250162044436891, '"TMSB10"': 0.05581814376350895, '"KRT19"': 0.04548687024222743, '"LGALS1"': 0.02419628358724785, '"MT-RNR1"': 0.021540918223268778, '"RPS19"': 0.019089578605601325, '"RPS14"': 0.014401267144233376, '"ENO1"': 0.013250379557480704, '"RPL13"': 0.012629847220402805, '"RPL35"': 0.008295266582972713, '"PKM"': 0.007644018041961665, '"MT-CO3"': 0.006913490199395791, '"MALAT1"': 0.006410534985500221, '"TPI1"': 0.005034188148293925, '"MT-ND4"': 0.004536968455553641, '"MT-ND3"': 0.004333515549134206, '"BCYRN1"': 0.004070369924364481, '"H4C3"': 0.004032532029166162, '"RPS5"': 0.0038543351696016023, '"MT-CYB"': 0.0035222760495261757, '"RPL12"': 0.0034849543641418206, '"RPL15"': 0.0032566606507516676, '"RPL30"': 0.0026747534742965966, '"RPL39"': 0.002488307578889406, '"RPL34"': 0.0022159112080691002, '"S100A10"': 0.002186966306547731, '"HES1"': 0.0021227411425202743, '"MT-ATP6"': 0.002093686746590384, '"RPLP1"': 0.0020557564452875067, '"RPLP2"': 0.0018795518343113589, '"DSP"': 0.0018362698293142253, '"RPS15A"': 0.001779134718985919, '"KRT18"': 0.0017285928000710772, '"RPS12"': 0.0015959186948774392, '"ROMO1"': 0.0015726059502340526, '"H2AC20"': 0.001569621300904654, '"TMEM64"': 0.0014243012821006321, '"PARD6B"': 0.0014236116912495138, '"ACTB"': 0.00135905465135564, '"SNRPD2"': 0.001342257975224724, '"SOX4"': 0.0013332769460236748, '"TMEM258"': 0.0013233936328404447, '"NEAT1"': 0.0013037871955105342, '"RPL36"': 0.0012940893193163672, '"RPS27"': 0.0012688288283579173, '"UQCRQ"': 0.001221864922154048, '"VMP1"': 0.0012189299376378858, '"TOB1"': 0.0012111390880236927, '"MT-ND2"': 0.0011460613569253795, '"RPS15"': 0.0010988834075067852, '"MT-CO2"': 0.0010985656307955997, '"RPL35A"': 0.0010620356471658329, '"RPS16"': 0.0009923818222538421, '"SET"': 0.0009867480686991746, '"PKIB"': 0.0009727192549003744, '"UBA52"': 0.0009091878826065128, '"COX7A2"': 0.0008858759488223066, '"RPL23"': 0.0008781821476895891, '"SERF2"': 0.0008214154520220867, '"HSPB1"': 0.0007999117853388814, '"MT-ND5"': 0.0007845747432649869, '"ATP5MK"': 0.0007842025861678688, '"ELOB"': 0.0007515379859932965, '"RPL37A"': 0.0007074142836545256, '"KRT8"': 0.000703914673027765, '"BPTF"': 0.0006405884007040398, '"COX7C"': 0.0006324780072910619, '"PFDN4"': 0.0006307913776681197, '"MGRN1"': 0.0006119447468571766, '"TRIM37"': 0.0006119135256725317, '"MT-ND4L"': 0.000608569926716786, '"TPD52L1"': 0.000594942106383743, '"MKI67"': 0.0005869357820648314, '"MT-ND6"': 0.0005769621119021687, '"RPL11"': 0.0005665868614178883, '"BCAS3"': 0.0005661873718244614, '"MT-ND1"': 0.0005604975108518916, '"TFF3"': 0.0005551987881785038, '"RPS28"': 0.0005543900968353746, '"PSMA7"': 0.0005504761480183636, '"PRRC2C"': 0.0005487681738150474, '"ATP5ME"': 0.000539377346114509, '"HNRNPA2B1"': 0.0005292131201116971, '"RPS6KB1"': 0.0005248771243887997, '"ANP32B"': 0.0005148148222521961, '"CALM2"': 0.0005021741008326336, '"NCL"': 0.00047760177658510197, '"CAPZA1"': 0.0004753058349470899, '"FTL"': 0.0004734340755928249, '"GPM6A"': 0.00047217567626078486, '"MT-CO1"': 0.00047181723701306675, '"NDUFB2"': 0.0004554004092272626, '"DSCAM-AS1"': 0.000446377037357132, '"MT-ATP8"': 0.0004393755579204549, '"H1-4"': 0.00043013318949180465, '"RPL29"': 0.0004293957940939237, '"S100A11"': 0.0004220353292370429, '"PLEC"': 0.00041177456584027086, '"H1-5"': 0.00040350201989146833, '"HNRNPUL1"': 0.0004027346153410169, '"HNRNPU"': 0.0003999522400173901, '"EIF4G2"': 0.00039853882978460787, '"PABPC1"': 0.0003805776424325268, '"C2CD2"': 0.0003790278172963413, '"CAST"': 0.0003771400329378565, '"DNAJA1"': 0.0003696690369188868, '"RPL28"': 0.0003671475391749197, '"ZNF217"': 0.00036671429732566813, '"NEDD8"': 0.0003602580273947408, '"CSDE1"': 0.0003565286009951728, '"TPM4"': 0.0003429138768467658, '"GOLGA4"': 0.0003351931829464771, '"CBX3"': 0.0003328748989399364, '"MT2A"': 0.0003272209675293793, '"CKS2"': 0.00032180313966078544, '"YWHAB"': 0.00031596585369802143, '"RPL37"': 0.0003158559531213767, '"HDGF"': 0.0003093864253314057, '"R3HDM1"': 0.0003085568903792137, '"JAK1"': 0.0003012974811918042, '"NCOA3"': 0.0002994401207047055, '"CDV3"': 0.00029938516317198514, '"RBM25"': 0.0002970301402400427, '"ANKIB1"': 0.0002970010287915743, '"PDAP1"': 0.00029634731726589696, '"ZC3H15"': 0.00029199344677337686, '"EBAG9"': 0.00029022425970124305, '"H2BC4"': 0.00028725248970738976, '"H2AC11"': 0.00028340813269391285, '"WSB2"': 0.00028133775429150897, '"TARS1"': 0.0002799115262407212, '"SPATS2L"': 0.0002729768018776204, '"HSPD1"': 0.0002713529452473577, '"SMC4"': 0.0002707105906987458, '"TPM3"': 0.000269721542064646, '"NCOR2"': 0.0002691811570273063, '"ENAH"': 0.0002691547609273413, '"INTS3"': 0.0002685043401226901, '"ATAD2"': 0.00026786444540006485, '"GATA3"': 0.0002631425388969223, '"H1-3"': 0.00026089307192039563, '"SPDL1"': 0.00025968729704659076, '"BASP1"': 0.00025956396250905443, '"HSPH1"': 0.00025764469712436953, '"RTF1"': 0.0002573111670777858, '"HMGB2"': 0.00025354623486413227, '"XBP1"': 0.0002523973243939284, '"DNMT3A"': 0.0002519317170803911, '"KIF5B"': 0.00025188761423593003, '"TIMM8B"': 0.00025062201889645606, '"HAND2-AS1"': 0.00024980531306380163, '"ANP32E"': 0.0002489807594711391, '"FGF23"': 0.00024581608874889587, '"EIF5B"': 0.000244822359238191, '"VPS4A"': 0.00024200016387393807, '"MRPS34"': 0.00024143030589071716, '"GSPT1"': 0.0002397332684808135, '"ATP1A1"': 0.00023876334493562088, '"C7orf50"': 0.00023790633863817717, '"H2AC12"': 0.00023566473790260307, '"STRBP"': 0.000235636020172236, '"HNRNPAB"': 0.00023516699919386594, '"NINJ1"': 0.0002351240407495706, '"CEP55"': 0.000234448414208099, '"IGFBP5"': 0.00023322811912098303, '"FBP1"': 0.00023238571227253573, '"PMEPA1"': 0.00023107437573306104, '"PKP4"': 0.00022905986642862924, '"CHMP4B"': 0.00022642525401003101, '"DEK"': 0.00022636069314335738, '"YWHAZ"': 0.0002259700416510612, '"PAK2"': 0.00022506872353198726, 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0.00019503186716691623, '"ZIC2"': 0.00019287260479161226, '"PTP4A2"': 0.0001920839832852421, '"NOSTRIN"': 0.00019118464771959598, '"H1-0"': 0.0001903268456320905, '"MCL1"': 0.00018890179808715572, '"PMS2CL"': 0.0001872077683779951, '"GTF2F1"': 0.0001866016761085387, '"CACNA1A"': 0.00018617860716819957, '"ZNF316"': 0.00018604237249900867, '"ZHX3"': 0.00018555870318430595, '"MYO10"': 0.00018549375994077674, '"ZFAND2A"': 0.0001850788753196073, '"CLIP1"': 0.00018497345222558297, '"SSRP1"': 0.00018429836309303345, '"ILF3"': 0.0001824550786119753, '"LARP1"': 0.00018179542275322924, '"AFG3L1P"': 0.00018173633326742475, '"PHF3"': 0.00018165277220933177, '"FARSA"': 0.000181633433313012, '"SLC9A3R1"': 0.00017835929609207277, '"MYBL1"': 0.00017712122747618936, '"MLYCD"': 0.000176748029348597, '"GASK1B-AS1"': 0.00017665659624727708, '"PREX1"': 0.00017497612280886174, '"MDM4"': 0.0001744730688856348, '"UBE2Q1"': 0.00017438751233874347, '"RCC2"': 0.00017391789618867706, '"KIAA0895L"': 0.00017225508532757057, '"USP32"': 0.00017221628280087697, '"C14orf28"': 0.00017215811680132038, '"RPS27L"': 0.0001720235894927778, '"SUPT6H"': 0.00017180672748813152, '"C9orf78"': 0.00017178936597413472, '"ATXN1L"': 0.00017137730297916813, '"EIF2AK2"': 0.00017016149598970474, '"METAP2"': 0.0001696359075665409, '"ATP6V1E1"': 0.0001687326231389183, '"G6PD"': 0.00016869602832325577, '"BMS1"': 0.0001686892861385436, '"LEO1"': 0.00016854576136758392, '"ABCB9"': 0.0001680768768057659, '"MED13"': 0.00016801694393030395, '"SESN2"': 0.00016712110349398305, '"PLEKHF2"': 0.00016693096734180627, '"NEDD4L"': 0.0001667046175599675, '"HBEGF"': 0.00016648755105685018, '"RNF4"': 0.00016537762422938094, '"NSD1"': 0.00016439800633489925, '"NMT1"': 0.00016409747805523056, '"PSMD14"': 0.00016338421696269803, '"BRIP1"': 0.0001631607189419457, '"ZNF767P"': 0.00016314628505112078, '"UHRF1BP1"': 0.00016293480634523675, '"NOTCH2NLC"': 0.00016134094656115386, '"HCFC1"': 0.0001612146683470319, '"CNOT2"': 0.00016069278746845225, '"MAP7"': 0.00015969635310212268, '"FAM47E"': 0.00015867799901505671, '"DNMT1"': 0.00015819407005613937, '"ARHGEF2"': 0.00015818777913266196, '"POLDIP2"': 0.00015776517021147838, '"NEMP1"': 0.00015764827997753812, '"NAA15"': 0.00015716432611477662, '"ZMYND11"': 0.00015650563938276625, '"AP3D1"': 0.00015650093666725538, '"TMEM218"': 0.00015634021968518035, '"ZNF302"': 0.00015538353007527362, '"SYNE2"': 0.0001536285820420611, '"AREG"': 0.00015330959616750503, '"SRP14-DT"': 0.0001530242036126214, '"PRKACA"': 0.00015249326334320756, '"IRX2"': 0.0001523012026191761, '"TASOR"': 0.0001511887298966543, '"EIF3A"': 0.00015091913953529812, '"ZNF347"': 0.0001501235357919199, '"TOP2A"': 0.00014983681978706043, '"EGR1"': 0.00014979934813940247, '"BTN3A2"': 0.00014959565130910532, '"BOD1L1"': 0.00014934257508358005, '"EPB41L1"': 0.0001489894806199391, '"FKBP5"': 0.0001482442660550128, '"EIF1AD"': 0.00014809129484646334, '"PLA2G15"': 0.00014728692615475743, '"RB1CC1"': 0.000147104908218223, '"TASOR2"': 0.0001456315139732506, '"UGDH"': 0.00014549865964405879, '"PLEKHN1"': 0.00014487647905136365, '"POLE"': 0.0001435257794317953, '"SMOX"': 0.0001434092368362807, '"LRCH3"': 0.0001430885287082032, '"SEMA4C"': 0.0001429726269884235, '"ABHD16A"': 0.00014294860153386523, '"PRR34-AS1"': 0.00014281045914166438, '"RHOD"': 0.000142768857069748, '"WASH3P"': 0.00014264336388033845, '"CNBP"': 0.00014219648484407285, '"LAT2"': 0.0001417665192271411, '"SPRYD3"': 0.00014156232187363752, '"ZC3H18"': 0.00014123504211593956, '"CAMSAP2"': 0.00014101040009929287, '"VAV2"': 0.00014056360803753516, '"SGO1"': 0.00014053962311675152, '"NEB"': 0.0001404995080547238, '"AAMP"': 0.00014032998351182232, '"SUDS3"': 0.00014008498106501084, '"PHACTR2"': 0.0001399006757291054, '"POLR2I"': 0.00013897914200694178, '"ATN1"': 0.00013891987448195486, '"ARF3"': 0.0001384990225906647, '"UQCC2"': 0.00013832675593241828, '"NET1"': 0.00013689621908047158, '"GUCD1"': 0.00013611063843656818, 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0.00012237819762943018, '"SMIM10L1"': 0.00012186795537431444, '"METRN"': 0.00012186221648211889, '"DGKZ"': 0.0001218593392702712, '"REV3L"': 0.00012177599490359738, '"PACS2"': 0.00012173277615854301, '"CALML5"': 0.00012171708752429533, '"UBALD1"': 0.00012168744164117445, '"MARK3"': 0.0001216535309529742, '"ZBTB7A"': 0.0001214092712094005, '"KCNC3"': 0.00012139589696638134, '"NBN"': 0.00012115478625729516, '"SCYL2"': 0.00012081642734540441, '"ATRX"': 0.00012033221140065063, '"TWNK"': 0.00011996605676057783, '"FZD1"': 0.00011960639226999541, '"H1-2"': 0.00011951890005281567, '"LINC02609"': 0.00011950200025443125, '"BAZ1B"': 0.00011697306538005129, '"BTBD9"': 0.00011664654803866613, '"ZBTB10"': 0.00011651709423718943, '"SMIM27"': 0.00011634613793954073, '"RBBP8"': 0.00011521149018077003, '"ANKRD11"': 0.00011510648236847668, '"CDC42BPB"': 0.00011490201678819606, '"TMEM63C"': 0.00011467675082554976, '"PABPC4"': 0.00011465157651832926, '"PUS7"': 0.00011419175849833968, '"ZNF703"': 0.00011391981334469736, '"ARHGAP5"': 0.00011307395411098766, '"BAZ2A"': 0.00011306057383422523, '"C20orf27"': 0.00011289023695060856, '"RBM23"': 0.00011261399017171288, '"HTATSF1"': 0.00011235838731254191, '"WDR43"': 0.00011235049639613236, '"RAB39B"': 0.00011231704900326813, '"PLBD2"': 0.00011217139588780125, '"CENPF"': 0.00011201171735312281, '"BCCIP"': 0.00011171741862667493, '"METRNL"': 0.00011170544639202552, '"GCLC"': 0.00011132379165884548, '"FAM102A"': 0.00011089788867047482, '"PPM1G"': 0.00011049459913341655, '"CASP8AP2"': 0.00011031434764800294, '"ISCU"': 0.00011019552490856381, '"ZNF219"': 0.000109812809345363, '"PSME4"': 0.0001088224889689461, '"TCF7"': 0.00010880562316220235, '"MTND1P23"': 0.00010859879080036091, '"SOS1"': 0.00010832504375723457, '"POLR2J"': 0.00010780517932499065, '"FUBP3"': 0.0001074402417044965, '"RAB12"': 0.00010743275376137478, '"NFX1"': 0.00010687120020127263, '"ROCK2"': 0.00010627498161163756, '"YTHDF1"': 0.00010585406734051894, '"ARHGAP1"': 0.00010549057563099448, '"STARD10"': 0.00010489833892958428, '"TRIP12"': 0.00010480530801090686, '"SMIM15"': 0.00010454752289602937, '"PABPN1"': 0.00010431420391493988, '"YES1"': 0.00010408150739053644, '"ARHGAP11A"': 0.00010398599337443566, '"CCDC51"': 0.00010376009526347104, '"C2CD2L"': 0.00010371317486044298, '"ETAA1"': 0.00010361667849781364, '"CDC37"': 0.0001036066468500555, '"SOGA1"': 0.00010341639149835414, '"ZNF146"': 0.00010322918641536364, '"PAPOLA"': 0.00010240647689524124, '"PSMD5"': 0.00010233807586924854, '"FBXL18"': 0.00010207301617509185, '"SYTL4"': 0.0001020374310096574, '"MT-TD"': 0.00010164594409496931, '"RP9"': 0.00010154489620154955, '"ASAH2B"': 0.00010152202178833303, '"C4orf48"': 0.00010077637014630758, '"RRP1B"': 0.00010026587977386188, '"SLAIN2"': 0.00010014364547080167, '"PRMT2"': 0.00010005113460922467, '"FRS2"': 9.984208385672964e-05, '"KPNA1"': 9.96865542867638e-05, '"AP2S1"': 9.949880811103417e-05, '"POLR3E"': 9.943255748875117e-05, '"NSD2"': 9.94145081371205e-05, '"RIPK2"': 9.938984152654767e-05, '"SETD1B"': 9.928725567831308e-05, '"SPIRE1"': 9.921759136628771e-05, '"DDX21"': 9.86297210421011e-05, '"WWP1"': 9.850986566472096e-05, '"CLK2"': 9.846947310784223e-05, '"GABPB2"': 9.836558034661554e-05, '"PLXNA1"': 9.804409747876841e-05, '"BCAR1"': 9.797570829787166e-05, '"ZC3H13"': 9.778971444113655e-05, '"ADM2"': 9.771532806923903e-05, '"ETF1"': 9.76607545199728e-05, '"LYAR"': 9.717238237093245e-05, '"NFKBID"': 9.707593952739142e-05, '"REV1"': 9.703853959985417e-05, '"NCALD"': 9.678176578796205e-05, '"PRPF19"': 9.673268564702342e-05, '"CAMK2B"': 9.662339631098651e-05, '"MCRIP2"': 9.64785597134102e-05, '"DLX6-AS1"': 9.647571993995368e-05, '"EIF2AK1"': 9.60655747278969e-05, '"DKC1"': 9.597663665907311e-05, '"MGP"': 9.572117950461056e-05, '"DVL3"': 9.524340083539638e-05, '"LRRCC1"': 9.518393630906533e-05, '"CDIPT"': 9.518144688944163e-05, '"MT-TS1"': 9.479584868547502e-05, '"BTBD6"': 9.43338208653755e-05, '"DNAJC2"': 9.430509889095422e-05, '"CPSF2"': 9.359250846762835e-05, '"RBAK"': 9.304883346747918e-05, '"KCTD3"': 9.300577173737384e-05, '"GPATCH4"': 9.289756842494244e-05, '"PPP1R37"': 9.252880433469837e-05, '"PACS1"': 9.235967549967777e-05, '"MPDZ"': 9.234423476571939e-05, '"NGRN"': 9.23358315749992e-05, '"PATL1"': 9.227914363236036e-05, '"CAV1"': 9.188379818934595e-05, '"HCG18"': 9.099317237431269e-05, '"COPS9"': 9.09712298122568e-05, '"PGAM5"': 9.053836130580581e-05, '"DNAJC21"': 9.050270635847111e-05, '"C6orf62"': 9.049991686476077e-05, '"NFKB1"': 9.032452682029743e-05, '"TSHZ2"': 9.001068951858652e-05, '"CETN3"': 8.96585368477088e-05, '"PARD3"': 8.946439016620324e-05, '"ANKRD52"': 8.930639576691601e-05, '"SIM2"': 8.878792940492558e-05, '"RAD21"': 8.875025081723456e-05, '"PER1"': 8.785592128560609e-05, '"RNPS1"': 8.784568084819045e-05, '"MAFG"': 8.766742828390751e-05, '"PROSER1"': 8.741955464861619e-05, '"RAB1B"': 8.670233489350588e-05, '"CA2"': 8.669996718236906e-05, '"ADGRV1"': 8.626184020543786e-05, '"FAM83H"': 8.579024106259361e-05, '"PCGF3"': 8.5764844012459e-05, '"ITPRID2"': 8.529926648447964e-05, '"TMPRSS4"': 8.506231070445773e-05, '"SEPTIN11"': 8.497179098939327e-05, '"RAPGEF5"': 8.462646213933288e-05, '"SMC5"': 8.442032152122961e-05, '"CDC42SE1"': 8.427706408230701e-05, '"RAD23B"': 8.42646084015034e-05, '"MAGI3"': 8.422238442323452e-05, '"TFPI2-DT"': 8.404780921234208e-05, '"PCP4"': 8.383002459118635e-05, '"MYH9"': 8.382236551657123e-05, '"MBNL3"': 8.361582638724472e-05, '"PREB"': 8.343087876459568e-05, '"MT-TN"': 8.315498025060685e-05, '"YAF2"': 8.306991122682155e-05, '"CORO2A"': 8.296876356099326e-05, '"TPM1"': 8.296606208516193e-05, '"RRN3P1"': 8.274980245066899e-05, '"NR1H2"': 8.258467918099986e-05, '"SNX25"': 8.240322833530587e-05, '"SUMO3"': 8.238667642472182e-05, '"CBX4"': 8.230078454688803e-05, '"HIP1"': 8.22921361879877e-05, '"TRIM3"': 8.228801824495163e-05, '"STUB1"': 8.220033115168072e-05, '"EP400P1"': 8.218445468120242e-05, '"TOP1MT"': 8.212200157698518e-05, '"BLOC1S3"': 8.208834970422018e-05, '"LACTB2-AS1"': 8.199659035823088e-05, '"SLC35C2"': 8.196049376793647e-05, '"EFCAB14"': 8.177307744787985e-05, '"ARID1B"': 8.172466486241647e-05, '"PHF21A"': 8.152240428326437e-05, '"CEP131"': 8.137510709185944e-05, '"LRRC37A3"': 8.136188872365783e-05, '"MID2"': 8.135033858233936e-05, '"MGAT4A"': 8.1266275362643e-05, '"SLC47A1"': 8.117454656692065e-05, '"RAB5C"': 8.103954109388259e-05, '"CCDC186"': 8.098028946620726e-05, '"RYR3"': 8.096211650896681e-05, '"UBE2J1"': 8.090342656248551e-05, '"GADD45GIP1"': 8.058827782999723e-05, '"MIR99AHG"': 8.054699782136489e-05, '"TRAPPC14"': 8.042228261277775e-05, '"KIF13A"': 8.032352122514247e-05, '"PI4KB"': 8.026287527667007e-05, '"CACNA1H"': 8.018442690436661e-05, '"AZI2"': 8.014967916945824e-05, '"SETD3"': 8.014518807480744e-05, '"SLC25A23"': 8.009798687046344e-05, '"C12orf76"': 8.007264186297624e-05, '"USP7"': 7.968186625959201e-05, '"ZNF112"': 7.960099548826497e-05, '"IPPK"': 7.949030945943591e-05, '"OTUD7B"': 7.941452509821779e-05, '"SOX11"': 7.937936009297196e-05, '"CTBP2"': 7.922915349345628e-05, '"GRK6"': 7.918961506006094e-05, '"SEC14L2"': 7.918443174961075e-05, '"DTX3L"': 7.90396091618937e-05, '"CEBPB"': 7.895825209527754e-05, '"EIF3J"': 7.886586310011838e-05, '"YARS1"': 7.868224202685655e-05, '"REM2"': 7.847104964755297e-05, '"MAP3K9"': 7.834519201449633e-05, '"DBF4"': 7.829758052253427e-05, '"EIF4EBP2"': 7.818608770702665e-05, '"ZNF257"': 7.81510965153435e-05, '"SSX2IP"': 7.805491302271281e-05, '"MOB3A"': 7.79733557558803e-05, '"FARP2"': 7.781724184880798e-05, '"PLA2G12A"': 7.767993320360651e-05, '"FAM32A"': 7.765145043887659e-05, '"MAPKAPK2"': 7.760858500740998e-05, '"NIBAN2"': 7.738191716013104e-05, '"AMOTL1"': 7.7296478773675e-05, '"ADD2"': 7.727483476569753e-05, '"PIK3CB"': 7.712490589314193e-05, '"ZHX1"': 7.695460308399374e-05, '"SMPD4BP"': 7.693154529604996e-05, '"NIPSNAP3A"': 7.665600456867681e-05, '"UBE2Q2"': 7.648829230896278e-05, '"TRIM44"': 7.64676013709883e-05, '"NCKAP1"': 7.642855242145654e-05, '"NIN"': 7.642589345280774e-05, '"KRT10"': 7.597865814289902e-05, '"NOMO3"': 7.578584083014445e-05, '"STARD7"': 7.55249413421444e-05, '"DPF1"': 7.546498998901216e-05, '"TLK2"': 7.544289576776854e-05, '"LRIF1"': 7.523387042578846e-05, '"TCHP"': 7.506901175127996e-05, '"AURKA"': 7.455701147759563e-05, '"LYPD4"': 7.428063306387437e-05, '"RGP1"': 7.423869977473672e-05, '"ODF2L"': 7.422873818113622e-05, '"RSRC2"': 7.352729035962747e-05, '"DHX16"': 7.32464990686437e-05, '"ARHGAP21"': 7.310685454249093e-05, '"ATXN7L1"': 7.294822470358506e-05, '"DHTKD1"': 7.281513440321467e-05, '"HNRNPD"': 7.273226921055944e-05, '"FBXW2"': 7.254426185085361e-05, '"SLTM"': 7.248148381446236e-05, '"C8orf88"': 7.207271853268296e-05, '"SRSF1"': 7.198489784183168e-05, '"GALNT1"': 7.197797085569973e-05, '"FRMD3"': 7.186655522490446e-05, '"INO80E"': 7.161580141275506e-05, '"LXN"': 7.152833007385177e-05, '"EIF2B4"': 7.140582117232049e-05, '"GHDC"': 7.102475825926716e-05, '"MARCHF6"': 7.063954711048261e-05, '"CTHRC1"': 6.998607286843767e-05, '"GTF3A"': 6.991377003553793e-05, '"QRSL1"': 6.988425510689017e-05, '"MRPL33"': 6.976511668077902e-05, '"LINC00885"': 6.956414338285323e-05, '"MAN1A2"': 6.953242737370256e-05, '"GNL3L"': 6.923234458246889e-05, '"ADAMTS19"': 6.921283022780747e-05, '"NDUFS6"': 6.918412549966338e-05, '"PDE8A"': 6.846963749007829e-05, '"PECR"': 6.822121253078497e-05, '"MAFA"': 6.82043769712283e-05, '"PPIG"': 6.807250117179044e-05, '"ZFP36L1"': 6.799397284971909e-05, '"TCL6"': 6.7024231261967e-05, '"INPP5A"': 6.696793869254485e-05, '"SLC25A24"': 6.692770150079249e-05, '"NCDN"': 6.635026263160749e-05, '"CTNNA1-AS1"': 6.63152706010363e-05, '"VAX2"': 6.6044260264068e-05, '"U2AF1L4"': 6.600028034921977e-05, '"RNF130"': 6.597610179864465e-05, '"SAP130"': 6.583176513119956e-05, '"WDFY3"': 6.574610727285282e-05, '"OR2I1P"': 6.567254904712095e-05, '"S100A9"': 6.563845557193025e-05, '"NAA10"': 6.546114588375473e-05, '"ZFC3H1"': 6.544112755772548e-05, '"SMG7"': 6.517323411246418e-05, '"PTGES3L"': 6.517100129914404e-05, '"LIMK1"': 6.487554424845965e-05, '"KCNJ3"': 6.468577956808307e-05, '"SLC25A37"': 6.450216579859549e-05, '"ILRUN"': 6.448530961929815e-05, '"KMT5B"': 6.362338495280632e-05, '"TBC1D22B"': 6.338084635703668e-05, '"SAMD8"': 6.321922574508851e-05, '"NMI"': 6.312310558762495e-05, '"TTYH1"': 6.302729724165778e-05, '"KPNB1P1"': 6.299998685124945e-05, '"OR2C3"': 6.283634327608711e-05, '"DPH1"': 6.276950657111282e-05, '"LINC02822"': 6.27250032326327e-05, '"ANKRD13D"': 6.270151310397094e-05, '"CEP128"': 6.269940652935993e-05, '"PCDHGA10"': 6.259187728150987e-05, '"MPHOSPH9"': 6.253388896672816e-05, '"LCA5L"': 6.251385431515782e-05, '"SPATA20"': 6.244928289348937e-05, '"SVIL-AS1"': 6.238430328469864e-05, '"ZNF574"': 6.237093436069876e-05, '"NACC1"': 6.234665715887303e-05, '"ZNF335"': 6.232672125685314e-05, '"CIAO3"': 6.22335756083433e-05, '"LIN54"': 6.223015826795796e-05, '"HAUS1"': 6.213553739800927e-05, '"ZZZ3"': 6.212519207011333e-05, '"SLC4A1"': 6.21183247233267e-05, '"MTRNR2L4"': 6.20966913866436e-05, '"CKMT1A"': 6.204579958699674e-05, '"RASSF3"': 6.199890550032824e-05, '"SLK"': 6.188931779162768e-05, '"PC"': 6.187110221518516e-05, '"SEPTIN8"': 6.185878907830524e-05, '"ZNF85"': 6.184008320152391e-05, '"BOLA3"': 6.181467181508393e-05, '"ZNF512B"': 6.179945978630752e-05, '"SKIDA1"': 6.173382061933026e-05, '"TGFB2"': 6.173186848311165e-05, '"OR2AT4"': 6.17095784327838e-05, '"LINC02913"': 6.169601231172892e-05, '"ZFP82"': 6.161429294500304e-05, '"MLX"': 6.159692188251962e-05, '"AKT2"': 6.149633303726799e-05, '"POLR2A"': 6.130097592904424e-05, '"PCLO"': 6.126651866218923e-05, '"MPP7"': 6.125286784123827e-05, '"TRIT1"': 6.109873949111234e-05, '"PITX1"': 6.109823414381652e-05, '"NDST1"': 6.101328107653825e-05, '"C5orf51"': 6.0962684364567766e-05, '"TARDBP"': 6.0908377689573654e-05, '"DNAJC3-DT"': 6.085670830235356e-05, '"FBXL20"': 6.073108104946669e-05, '"FBXO42"': 6.049888721816255e-05, '"FASN"': 6.034864843080965e-05, '"ARIH1"': 6.032303908026225e-05, '"MYBL2"': 6.031776032469167e-05, '"MIEN1"': 6.030781183432769e-05, '"LMNB2"': 6.022080585486983e-05, '"STK25"': 6.013838386308855e-05, '"DIO2"': 6.012162374817759e-05, '"PTPN23"': 6.0092740820993986e-05, '"WDFY2"': 6.009263512463498e-05, '"RENO1"': 6.006710878547899e-05, '"JADE3"': 6.004350663047343e-05, '"COL12A1"': 5.987747638054073e-05, '"TJAP1"': 5.9868976552579954e-05, '"PYGO2"': 5.975100569181869e-05, '"RIC1"': 5.9687063837224426e-05, '"KIF18B"': 5.964611043605201e-05, '"ELAC1"': 5.957865001937409e-05, '"CENPU"': 5.9507346487103614e-05, '"UBXN2B"': 5.946241723604375e-05, '"TMEM62"': 5.9044728141628134e-05, '"ALKBH5"': 5.904197278630901e-05, '"ZC3H10"': 5.8941884494597454e-05, '"WT1-AS"': 5.887398824165827e-05, '"CES2"': 5.877287799013771e-05, '"LETM1"': 5.876038367190777e-05, '"TNIP2"': 5.872496598840443e-05, '"ZNF2"': 5.8691297463046604e-05, '"NPM1P40"': 5.853520294812154e-05, '"EPN1"': 5.8528136561400486e-05, '"MASTL"': 5.845018525840056e-05, '"LTBR"': 5.840464508382373e-05, '"EPHX2"': 5.831840509246034e-05, '"CDHR3"': 5.8271605844642823e-05, '"UBE2E3"': 5.8110050037591134e-05, '"RHPN1"': 5.808849668824323e-05, '"ZNF688"': 5.797412816372021e-05, '"PRRT2"': 5.783581864628466e-05, '"RPS19BP1"': 5.776577848136669e-05, '"MYH14"': 5.761894392914144e-05, '"CNTRL"': 5.739286935880311e-05, '"MDM2"': 5.7310052625310703e-05, '"SINHCAFP3"': 5.722755165491257e-05, '"UIMC1"': 5.716070558350756e-05, '"IKBKG"': 5.715999379021551e-05, '"KIF21A"': 5.7006030577492045e-05, '"SLC25A28"': 5.6947653858856655e-05, '"TMEM184C"': 5.691179720163349e-05, '"MFN2"': 5.676010495653204e-05, '"TRAK1"': 5.666050278837947e-05, '"NDUFAF8"': 5.6621581534046306e-05, '"DDX28"': 5.659239411867736e-05, '"AGO1"': 5.648862140631726e-05, '"RBBP6"': 5.603419953846791e-05, '"PPRC1"': 5.572335536166955e-05, '"TAOK3"': 5.567705083380426e-05, '"IMPA1"': 5.566627414835785e-05, '"KPNA4"': 5.556299376344341e-05, '"HIF1A"': 5.5521762274971706e-05, '"ZNF77"': 5.548136527676154e-05, '"PKP1"': 5.5149275588023834e-05, '"FGD5-AS1"': 5.50591715371042e-05, '"CDC25B"': 5.495175042627629e-05, '"ROCK1"': 5.4747951039932336e-05, '"SRM"': 5.462527093694628e-05, '"CEP78"': 5.45971052721929e-05, '"ASB13"': 5.3868917077142796e-05, '"NRBP1"': 5.323491028380259e-05, '"TSHZ1"': 5.3164506719921815e-05, '"KIF1C"': 5.295831878105111e-05, '"PRKCD"': 5.2707237022709154e-05, '"SNORC"': 5.255850167995959e-05, '"PRXL2C"': 5.252964197649555e-05, '"PPP4R3A"': 5.227215509797377e-05, '"ARPP19"': 5.226650338478169e-05, '"HELB"': 5.2230387767448894e-05, '"SLC25A44"': 5.2158979365274606e-05, '"NSMCE4A"': 5.214766017441173e-05, '"GOLT1A"': 5.2137377113476906e-05, '"NAP1L6P"': 5.20503959267163e-05, '"DCAF6"': 5.168592107784057e-05, '"TUBE1"': 5.1598833848779267e-05, '"HMGN5"': 5.143080980653732e-05, '"FAM13B"': 5.1287669214709796e-05, '"LINC00491"': 5.1072646521016514e-05, '"ITGB8"': 5.106094203904864e-05, '"HYAL2"': 5.092899857087187e-05, '"ERBIN"': 5.0779633003247715e-05, '"SRGAP1"': 5.062065224453059e-05, '"LARP1B"': 5.029022182241114e-05, '"FAM111B"': 4.9428904090020305e-05, '"AFAP1"': 4.885970266243826e-05, '"TACC2"': 4.824352741413916e-05, '"KIF16B"': 4.821450306603317e-05, '"ZMIZ1"': 4.818738613956899e-05, '"RBM12B-AS1"': 4.802153899298641e-05, '"HMGA1"': 4.766894745311485e-05, '"ARHGEF37"': 4.763013271865275e-05, '"SPAG9"': 4.761743945561284e-05, '"EIF4E"': 4.72205371698331e-05, '"CCNB3P1"': 4.7126370487472036e-05, '"DDX25"': 4.701354991174263e-05, '"CMBL"': 4.673067421989999e-05, '"CEP104"': 4.596234927495134e-05, '"VMAC"': 4.575157576094303e-05, '"MIOS"': 4.544445197767513e-05, '"CAMK2D"': 4.51310685960653e-05, '"LRRC59"': 4.50861883625364e-05, '"PLCD3"': 4.4940194789933864e-05, '"SECISBP2"': 4.4849368291179506e-05, '"FNTA"': 4.4682727920275966e-05, '"PARP9"': 4.417287485867143e-05, '"PPP2R5D"': 4.417055339321728e-05, '"RAB23"': 4.3101541954957846e-05, '"STIMATE"': 4.240963188706826e-05, '"RAB13"': 4.238560428071055e-05, '"CDK6"': 4.225931635216539e-05, '"ST6GAL1"': 4.205497456231126e-05, '"SLC48A1"': 4.2054939368898064e-05, '"MIR3677HG"': 4.203424545491546e-05, '"VCAN"': 4.200085014193733e-05, '"SIX3"': 4.199896081035294e-05, '"ONECUT2"': 4.1967589528696916e-05, '"FBXW5"': 4.1963979591470425e-05, '"DONSON"': 4.196342269579762e-05, '"USP1"': 4.195516633916748e-05, '"LIN52"': 4.195214937934144e-05, '"SPSB1"': 4.192844398232104e-05, '"AMIGO1"': 4.1925899792146474e-05, '"PRTG"': 4.188522983986195e-05, '"WDR26"': 4.188215309154548e-05, '"GAS2L1"': 4.1869386508690953e-05, '"TNFAIP2"': 4.1864493046168554e-05, '"DPY19L1"': 4.1859775228075785e-05, '"MT-TA"': 4.1836355180991346e-05, '"CNOT3"': 4.1818388457474024e-05, '"CTSL"': 4.1817486025618734e-05, '"TLE2"': 4.1800686450497634e-05, '"TMEM69"': 4.178559729080704e-05, '"SP2"': 4.177638848141565e-05, '"RIPOR1"': 4.177431197370791e-05, '"DEDD"': 4.176370576160391e-05, '"ESS2"': 4.173748665380645e-05, '"TAOK1"': 4.173273476865265e-05, '"CASTOR2"': 4.173050330115919e-05, '"LINC01426"': 4.1727946768990506e-05, '"TTC7A"': 4.172701757027498e-05, '"PSORS1C1"': 4.1722414143575145e-05, '"NFATC3"': 4.1698420072318076e-05, '"MT-TS2"': 4.169221118178108e-05, '"KLC1"': 4.161223022867905e-05, '"SOX9-AS1"': 4.160746591129926e-05, '"BCL3"': 4.15738255701231e-05, '"ZBTB20"': 4.1572008870387546e-05, '"SYNJ2"': 4.156215501148486e-05, '"TTC38"': 4.1552567059410067e-05, '"KRT13"': 4.1542131936216255e-05, '"LNCARSR"': 4.1498738780204535e-05, '"MAILR"': 4.149037636485061e-05, '"FCHO1"': 4.148676839662161e-05, '"SLMAP"': 4.148095280946618e-05, '"ZBED5-AS1"': 4.1480528486635275e-05, '"ARHGEF26"': 4.146038267925103e-05, '"EIPR1"': 4.145345306853627e-05, '"MT1F"': 4.1452234474611557e-05, '"SPIN1"': 4.145147339896734e-05, '"PTGES2"': 4.144423253660511e-05, '"WNT7B"': 4.1433623438101614e-05, '"CMTM3"': 4.143341495913579e-05, '"TWF2"': 4.1428235717054e-05, '"MDM1"': 4.142364025718618e-05, '"PCBP3"': 4.141914234674223e-05, '"TMEM191C"': 4.138491226589154e-05, '"CRNDE"': 4.1378432849658e-05, '"H2AZ2P1"': 4.1375583966812904e-05, '"LDLRAP1"': 4.1360541889195344e-05, '"SNHG12"': 4.1358610053350914e-05, '"GALNT18"': 4.1358300368682034e-05, '"MIPOL1"': 4.135644785600381e-05, '"BOK"': 4.133567382179162e-05, '"MNT"': 4.132636818713747e-05, '"GRAMD4P3"': 4.132463097886228e-05, '"MAMLD1"': 4.131761769177028e-05, '"CABLES1"': 4.131045272272934e-05, '"ABCD4"': 4.128161283242542e-05, '"PROM2"': 4.1275065323146097e-05, '"RPS6KA4"': 4.1269436727888195e-05, '"PAQR3"': 4.1228210879541e-05, '"KRT16"': 4.1222257094683175e-05, '"MYO1F"': 4.119832931344102e-05, '"STX3"': 4.1181988143172346e-05, '"OR7E13P"': 4.117743174151313e-05, '"ATP6V0D1-DT"': 4.117526284101171e-05, '"ZBTB42"': 4.11468674758734e-05, '"SDHAF2"': 4.113396631991062e-05, '"TEX261"': 4.113178804174977e-05, '"SLC9A3-AS1"': 4.112431014916358e-05, '"PLEKHB2"': 4.111868977304638e-05, '"COTL1"': 4.111586040458754e-05, '"PCED1B-AS1"': 4.111375571107388e-05, '"ZWILCH"': 4.1066890654059134e-05, '"LINC02605"': 4.10565370687119e-05, '"MARK2"': 4.1054852549574845e-05, '"CNIH3"': 4.1016996296695624e-05, '"FAM177A1"': 4.1010795389689424e-05, '"LINC00345"': 4.100481073479565e-05, '"RABEP1"': 4.0999013413375816e-05, '"BROX"': 4.0993745194520916e-05, '"SMARCD2"': 4.097490352824714e-05, '"GIPR"': 4.093569671842591e-05, '"TMSB4XP4"': 4.0935463158615485e-05, '"NAA50"': 4.090595974248145e-05, '"TPP1"': 4.090091561012115e-05, '"POMK"': 4.087786091348404e-05, '"PDCD6IPP2"': 4.0850846846552054e-05, '"NACC2"': 4.081460697010245e-05, '"MAP3K2"': 4.07842211235938e-05, '"WDR24"': 4.0776199343662464e-05, '"MRPL38"': 4.073956116508487e-05, '"KCNE4"': 4.073590353844109e-05, '"CFAP97"': 4.0732314022139945e-05, '"HSPD1P11"': 4.068600162657957e-05, '"PLAA"': 4.065859842755108e-05, '"KRT81"': 4.064710568845528e-05, '"LINC01488"': 4.063152268364425e-05, '"ITPK1"': 4.056931698137434e-05, '"MYEF2"': 4.049514170459076e-05, '"RFWD3"': 4.048148488373457e-05, '"MT-TC"': 4.048007038203678e-05, '"RAB3D"': 4.0402621542426695e-05, '"CAPN15"': 4.0373386531092e-05, '"MT-TE"': 4.0320080021582344e-05, '"BCR"': 4.0318382159021695e-05, '"CLDN15"': 4.031481175074307e-05, '"BICDL1"': 4.029818628030462e-05, '"TUBD1"': 4.029641346571077e-05, '"TNPO2"': 4.0292251451576744e-05, '"DCLRE1B"': 4.0256627287630445e-05, '"UBE2K"': 4.024196680151708e-05, '"CRYL1"': 4.0198393313454624e-05, '"ZNF329"': 4.0092165662316955e-05, '"MOB2"': 4.007594425840817e-05, '"LYPD6"': 4.007467795692191e-05, '"FBXL19"': 4.006718155090569e-05, '"GUCY1B2"': 4.00006384483388e-05, '"ERVMER34-1"': 3.99456169374027e-05, '"MIR4458HG"': 3.993251993045276e-05, '"ZNRF1"': 3.9923334473310204e-05, '"RALBP1"': 3.991844654100849e-05, '"GLE1"': 3.98787601748766e-05, '"CLSPN"': 3.980947730778672e-05, '"WDR5"': 3.975667336559496e-05, '"MTMR2"': 3.973563146844003e-05, '"RECQL4"': 3.9734587918233305e-05, '"SENP6"': 3.969930916561688e-05, '"TESK1"': 3.9592699381051244e-05, '"MYADM"': 3.9584173859579076e-05, '"CXADR"': 3.95741904791198e-05, '"EPS8L2"': 3.954470052041709e-05, '"SCARA3"': 3.950441748503334e-05, '"SSH3"': 3.950257127797192e-05, '"FMR1"': 3.933804503612847e-05, '"YJU2"': 3.9323762679152536e-05, '"XRCC2"': 3.9323040745102485e-05, '"F3"': 3.9317707859485304e-05, '"KCTD15"': 3.924070898611251e-05, '"PSMC5"': 3.921872495494099e-05, '"GOLGA5"': 3.9170470691136254e-05, '"FBXL4"': 3.914437684356535e-05, '"DCTN6-DT"': 3.909481651704449e-05, '"CHD8"': 3.903379263227481e-05, '"GAB2"': 3.901507735868688e-05, '"CEP83"': 3.894817764400047e-05, '"PLD6"': 3.884944411903769e-05, '"PHLDA2"': 3.881062038786274e-05, '"MAPK9"': 3.8808128643291615e-05, '"RRP15"': 3.872793060354155e-05, '"SLC25A43"': 3.870168469653623e-05, '"RASGEF1B"': 3.863124161763292e-05, '"SLC66A2"': 3.848472757126422e-05, '"C5"': 3.8482612675320215e-05, '"POGK"': 3.8466596678964945e-05, '"MICAL2"': 3.836901894804629e-05, '"SMC6"': 3.832089723039311e-05, '"EIF4G3"': 3.81305250435675e-05, '"VCPIP1"': 3.812311663311038e-05, '"POLD2"': 3.809988029555155e-05, '"LPP"': 3.8051054045982735e-05, '"RRAGC"': 3.80212746447229e-05, '"PICALM"': 3.7953916826993394e-05, '"FAM222B"': 3.789350876676902e-05, '"DNAJA3"': 3.780284959214709e-05, '"ALDH2"': 3.7668165846212834e-05, '"PTBP3"': 3.75756852684609e-05, '"MAEA"': 3.712372203757839e-05, '"ELOVL7"': 3.698979147423084e-05, '"DCTN5"': 3.685370060652758e-05, '"PRPS1"': 3.677854484471193e-05, '"SLC24A2"': 3.6594541443651655e-05, '"BDP1"': 3.6356219973032196e-05, '"ETNK1"': 3.62822178671456e-05, '"VRK3"': 3.626163214270277e-05, '"KCNG1"': 3.623676676807386e-05, '"TAF13"': 3.587426153960223e-05, '"TPCN1"': 3.568006366331317e-05, '"ERVK3-1"': 3.564335291473761e-05, '"KIAA1522"': 3.5556638571903576e-05, '"AHCYL1"': 3.541040499650153e-05, '"SNAPC2"': 3.5277666940325505e-05, '"FAM120A"': 3.521973506620912e-05, '"DOHH"': 3.503505381689361e-05, '"RIC8A"': 3.4958445639811775e-05, '"ZNF510"': 3.479248840113535e-05, '"CAMK2N1"': 3.461884514535043e-05, '"SAMD12"': 3.456697684652928e-05, '"DNAJC5"': 3.443189828629751e-05, '"SAPCD2"': 3.4389769387063105e-05, '"ITGB8-AS1"': 3.438804838533191e-05, '"BICD2"': 3.4343938177059395e-05, '"PATJ"': 3.4239143464934616e-05, '"SEPTIN9"': 3.416121443262958e-05, '"C11orf24"': 3.415144391378255e-05, '"RNF168"': 3.408701350860271e-05, '"UQCC3"': 3.376246597350026e-05, '"CRK"': 3.306359567744544e-05, '"MAPK8IP2"': 3.2684848597791694e-05, '"BCL2L15"': 3.260178679934653e-05, '"ZMYM3"': 3.246889569375728e-05, '"MAD2L1BP"': 3.187426774102608e-05, '"RGPD4-AS1"': 3.174990024629296e-05, '"MTMR12"': 3.173394138323789e-05, '"CMPK1"': 3.1440774343037374e-05, '"LINC01278"': 3.128697784333444e-05, '"PAK4"': 3.1247643817289385e-05, '"CALML3-AS1"': 3.094076195311798e-05, '"CMSS1"': 3.0549323727339554e-05, '"EEA1"': 3.0510320673472837e-05, '"DTX3"': 3.0501849656378872e-05, '"TIGAR"': 3.0393591095042994e-05, '"ATMIN"': 3.0232555502478104e-05, '"R3HDM2"': 3.0214180865815508e-05, '"FAM219B"': 3.0156180558462954e-05, '"CCNO"': 2.968781753187504e-05, '"POLB"': 2.9394354335308372e-05, '"NETO2"': 2.9101241276813864e-05, '"LCMT1"': 2.902466498419912e-05, '"SLC35C1"': 2.8564617313909615e-05, '"RAB35"': 2.838059629967166e-05, '"GCC2"': 2.827179518745426e-05, '"KLHL7"': 2.813902697621563e-05, '"ULK1"': 2.7973311326386642e-05, '"ZDHHC7"': 2.780130499915894e-05, '"TRIM41"': 2.7685789313721683e-05, '"CCNYL1"': 2.7540180160804092e-05, '"SOX7"': 2.7529355747907695e-05, '"GCNA"': 2.7464134905785622e-05, '"ZNF572"': 2.741513349653836e-05, '"IFI27"': 2.73261215826236e-05, '"GYG1"': 2.7076016616124983e-05, '"APOOL"': 2.6879263303687306e-05, '"JPH3"': 2.6824673828710097e-05, '"OTULIN"': 2.6738815971026563e-05, '"FBXO11"': 2.6474472235843126e-05, '"DOCK8-AS1"': 2.6370677204777762e-05, '"TTLL12"': 2.6162263720678197e-05, '"BOP1"': 2.615861226215584e-05, '"EDA"': 2.6133294806911026e-05, '"KIF3B"': 2.541373377080176e-05, '"SCRIB"': 2.5387153106590312e-05, '"PLAGL1"': 2.5275244010494252e-05, '"PCGF2"': 2.4838077881736066e-05, '"TMEM178B"': 2.47533755736443e-05, '"CSK"': 2.417134469265241e-05, '"FLVCR2"': 2.3921200820812403e-05, '"ZNF442"': 2.333158098836578e-05, '"CPEB4"': 2.2216093803650572e-05, '"PTPDC1"': 2.20564384183771e-05, '"PHKG2"': 2.175463473113577e-05, '"NUP62"': 2.1207794984268775e-05, '"TRIP13"': 2.1180577300702177e-05, '"ZNF232"': 2.1177604006443596e-05, '"KLC2"': 2.1175401866422114e-05, '"TEPSIN"': 2.116226821251515e-05, '"REST"': 2.115921116735739e-05, '"CNDP2"': 2.1147166106301412e-05, '"TGFB3"': 2.1146504278664372e-05, '"VDR"': 2.1135224820002353e-05, '"PANK4"': 2.1131552874328338e-05, '"NKIRAS2"': 2.1128009583681144e-05, '"GPATCH3"': 2.1127816693688747e-05, '"TRERF1"': 2.1125603414979657e-05, '"SLC4A11"': 2.1119247074663946e-05, '"STX2"': 2.1111253174911257e-05, '"ZNF772"': 2.11075489155453e-05, '"DENND1B"': 2.1105834431459793e-05, '"CNOT6L"': 2.110486629936818e-05, '"TSPAN33"': 2.109437306243696e-05, '"GPR85"': 2.1090186445190995e-05, '"LINC00173"': 2.1087207462978478e-05, '"PARVB"': 2.1086179267272994e-05, '"AVEN"': 2.1083772791378315e-05, '"TMEM164"': 2.1082246772603578e-05, '"TRMT2A"': 2.1080582584411277e-05, '"SALL4"': 2.1080137357859023e-05, '"ZNF121"': 2.107813769632773e-05, '"MEX3D"': 2.107077699297614e-05, '"FAAP100"': 2.1070403544816334e-05, '"PLCB4"': 2.106126172880751e-05, '"ZNF626"': 2.106111221532704e-05, '"TM4SF19-AS1"': 2.1061066136423937e-05, '"ALDH4A1"': 2.105668905525349e-05, '"ZNF620"': 2.105416951294066e-05, '"SYT14"': 2.1049657621851686e-05, '"JMJD8"': 2.1047067743561676e-05, '"DCAF4"': 2.104288305422023e-05, '"MT-TL1"': 2.1041136178658526e-05, '"MAP3K12"': 2.1036802818495805e-05, '"PHACTR1"': 2.103669099083971e-05, '"DEAF1"': 2.103505169699975e-05, '"AFF1"': 2.1034042690119373e-05, '"INPP5E"': 2.1032507135563108e-05, '"NUP98"': 2.1032242006113392e-05, '"TNS2"': 2.103154437940148e-05, '"ARID4B"': 2.1030991516077698e-05, '"KCNJ6"': 2.1027037042564393e-05, '"FAM104A"': 2.102551527309377e-05, '"CDC42BPA"': 2.1025489496434007e-05, '"ZNF134"': 2.1018877554798446e-05, '"RNF180"': 2.1017777321374008e-05, '"ABL1"': 2.1015649033304143e-05, '"TXNRD2"': 2.1011354692395086e-05, '"GPN1"': 2.10097627518752e-05, '"DCAF10"': 2.1009398569906258e-05, '"ANKH"': 2.100841156077055e-05, '"NFATC2"': 2.100621351977524e-05, '"POTEC"': 2.100581598441841e-05, '"IER5L"': 2.1004689443868106e-05, '"ACKR3"': 2.1004678928663263e-05, '"VAT1"': 2.1002119371547677e-05, '"GCAT"': 2.1001993941650943e-05, '"ZNF777"': 2.0999764750173554e-05, '"PPOX"': 2.099568849093021e-05, '"APOBEC3F"': 2.099357109711859e-05, '"CEP63"': 2.0987979532241063e-05, '"NLK"': 2.0987687286981888e-05, '"RHOU"': 2.0984548363481343e-05, '"DUSP8"': 2.0984069109925777e-05, '"VPS54"': 2.0982085577624848e-05, '"VPS9D1-AS1"': 2.0979407533187898e-05, '"TMEM80"': 2.097610152854098e-05, '"ULK3"': 2.097543528039283e-05, '"NEUROD2"': 2.0975148491999175e-05, '"CYB561D2"': 2.0974847941534434e-05, '"NPTN"': 2.0972498742894682e-05, '"LPCAT4"': 2.0970268095751868e-05, '"FAM86EP"': 2.0969343567247435e-05, '"PATZ1"': 2.096679731399293e-05, '"SRFBP1"': 2.0965005778353975e-05, '"MC2R"': 2.0964432058991023e-05, '"PSMD13"': 2.0963634004684424e-05, '"MYO3B-AS1"': 2.0963457829931104e-05, '"FAM20C"': 2.0962683736107358e-05, '"RPL12P38"': 2.0961512564308405e-05, '"NAGLU"': 2.095994652072809e-05, '"PTPN13"': 2.0959578031836385e-05, '"ITSN1"': 2.0957020390249198e-05, '"ERVK13-1"': 2.095587177496366e-05, '"MAN1C1"': 2.0951562140009373e-05, '"FAM189B"': 2.0950751873514164e-05, '"MGLL"': 2.0949394553416738e-05, '"ZZEF1"': 2.0945491006926852e-05, '"SMIM5"': 2.0945069988088533e-05, '"ELP3"': 2.0943090714971385e-05, '"PCAT1"': 2.0942800998892587e-05, '"TCHH"': 2.0942070509225395e-05, '"TMEM222"': 2.0941570235338585e-05, '"RFFL"': 2.094155236422879e-05, '"CERS4"': 2.0941439836069775e-05, '"BRMS1L"': 2.0938743563113223e-05, '"TBC1D9"': 2.0937283929506354e-05, '"ATP1A4"': 2.093675441068902e-05, '"NCOA2"': 2.0936532033571205e-05, '"ORAI1"': 2.0935972709187955e-05, '"MMD"': 2.0934684906982295e-05, '"KMT2D"': 2.0934533070479004e-05, '"HELZ2"': 2.0932190613561616e-05, '"ABHD1"': 2.0930820330986274e-05, '"ABCC4"': 2.0929604893957845e-05, '"SLC25A25-AS1"': 2.0929154815219718e-05, '"DPY19L1P1"': 2.0926548384984005e-05, '"SIX4"': 2.0926117858917117e-05, '"CDH6"': 2.0926004825178782e-05, '"HMGB1P51"': 2.092453363008472e-05, '"ESRP2"': 2.09234394932872e-05, '"CCNY-AS1"': 2.091942932228465e-05, '"ABLIM1"': 2.0917057267696935e-05, '"TRIM14"': 2.0916083629108834e-05, '"SENP7"': 2.091583924794596e-05, '"MT-TP"': 2.091433587874354e-05, '"ZNF579"': 2.0909586531001877e-05, '"CALR4P"': 2.0907815492075294e-05, '"CAMKK2"': 2.0905200666779556e-05, '"LCORL"': 2.0904706060859862e-05, '"LIAS"': 2.0893467047586364e-05, '"NOP2"': 2.0891709252971997e-05, '"FN3K"': 2.0891260730772364e-05, '"IRS3P"': 2.0889599558414017e-05, '"OR9H1P"': 2.0889165529881326e-05, '"IGDCC3"': 2.088047720922826e-05, '"EPHB4"': 2.0877804293886503e-05, '"TUT4"': 2.0872012124005314e-05, '"FGF12"': 2.0871494352025445e-05, '"RADIL"': 2.0870824420730917e-05, '"RC3H2"': 2.0867768909524927e-05, '"NBEAL2"': 2.0866668659849488e-05, '"AQP11"': 2.0865733774845014e-05, '"KYAT3"': 2.086564836707798e-05, '"WIPI2"': 2.0859903523642346e-05, '"CLEC16A"': 2.0856878988835095e-05, '"AFF4"': 2.0851433167125064e-05, '"MED25"': 2.0850496130166625e-05, '"KCTD18"': 2.0842807435925668e-05, '"GSE1"': 2.0838583218742363e-05, '"FBXO30"': 2.0838262832132234e-05, '"TMEM115"': 2.083407157655607e-05, '"CCM2"': 2.0831842957580174e-05, '"CCNT2-AS1"': 2.0831385193264815e-05, '"BAGE2"': 2.0826955453490343e-05, '"THEM4"': 2.0826087262503284e-05, '"NAT8L"': 2.0821489749807745e-05, '"SLC43A2"': 2.0820592412347e-05, '"HES6"': 2.081834270293025e-05, '"YRDC"': 2.081585788695214e-05, '"MAP2K5"': 2.0814769255592027e-05, '"PPT2"': 2.0809648740482917e-05, '"B9D1"': 2.080721049288026e-05, '"GAREM1"': 2.080623211473077e-05, '"KMT2B"': 2.080547014098906e-05, '"LINC00844"': 2.0796320803405252e-05, '"DUSP7"': 2.079413762749336e-05, '"SLC36A4"': 2.0794031761655143e-05, '"GRIPAP1"': 2.0784476064994202e-05, '"SHISA2"': 2.0780987894753832e-05, '"TP53BP2"': 2.0779602813759645e-05, '"PRMT6"': 2.0776678252577653e-05, '"HMGN1P14"': 2.077601459316964e-05, '"TPPP3"': 2.0774626087080578e-05, '"CDK12"': 2.077245086672717e-05, '"MMP25-AS1"': 2.0766878586764208e-05, '"FBXO27"': 2.076534900426496e-05, '"PLCB1"': 2.0763106623607375e-05, '"FMN1"': 2.0761465104747515e-05, '"F8"': 2.0760668617492763e-05, '"PCDHB4"': 2.075687347574915e-05, '"KLHL22"': 2.074754406866178e-05, '"ZNF254"': 2.0746844690215974e-05, '"FOXK2"': 2.074537684513541e-05, '"IPO5P1"': 2.0742468802751938e-05, '"DIABLO"': 2.0741897996440507e-05, '"OTUB2"': 2.0741410747558938e-05, '"GTPBP2"': 2.0732428891944286e-05, '"LINC01725"': 2.0726163240855794e-05, '"NEK8"': 2.072577121497048e-05, '"PIP4K2A"': 2.072194079080454e-05, '"OGN"': 2.071985645431565e-05, '"MAPKAPK5"': 2.0717717747936255e-05, '"ZNF512"': 2.071089093316712e-05, '"NDUFA6-DT"': 2.0710201621106356e-05, '"EN2"': 2.0709689059681033e-05, '"DTYMK"': 2.0709303135111052e-05, '"RASAL1"': 2.0699633578294426e-05, '"PCDHGB6"': 2.0698934712987065e-05, '"PSMF1"': 2.069657318605929e-05, '"KIF9-AS1"': 2.069473880765379e-05, '"LINC01291"': 2.0692454802909053e-05, '"RBM15B"': 2.0682752992387867e-05, '"NAA16"': 2.0675190010317052e-05, '"ACTR5"': 2.067375023082593e-05, '"ZNF879"': 2.0667782698220923e-05, '"BRF1"': 2.0663885716522327e-05, '"FMNL3"': 2.0663776044790453e-05, '"CTNS"': 2.06602601516309e-05, '"ZADH2"': 2.0659621128223297e-05, '"SCMH1"': 2.0650596532194132e-05, '"ARL17B"': 2.0648320714905126e-05, '"BRPF3"': 2.0646356924973933e-05, '"FBRSL1"': 2.0640155327914795e-05, '"KIFC2"': 2.0640141460434965e-05, '"ABHD3"': 2.06354844966806e-05, '"TEDC2-AS1"': 2.0635286449224795e-05, '"GPR132"': 2.0617462028476732e-05, '"DUS4L"': 2.0614850657518732e-05, '"MAP3K14-AS1"': 2.060460962648021e-05, '"ANKRD20A5P"': 2.060264641603972e-05, '"CASP10"': 2.0601135844070366e-05, '"ZNF326"': 2.0598984778230372e-05, '"PRR12"': 2.059770382596343e-05, '"ARHGAP39"': 2.059693292301483e-05, '"GMCL1"': 2.059527305450682e-05, '"WNK1"': 2.058953193381637e-05, '"TMCO6"': 2.0589531933816316e-05, '"CSKMT"': 2.0585910869464883e-05, '"BAG1"': 2.058403630826087e-05, '"ZNF154"': 2.0583169818704647e-05, '"SDCBP2-AS1"': 2.05799753180846e-05, '"UBP1"': 2.0561220268631438e-05, '"RPLP0P2"': 2.0560807760890073e-05, '"VASH1"': 2.0560172569767022e-05, '"VPS52"': 2.0513279278500714e-05, '"L2HGDH"': 2.0505143909064208e-05, '"SACS"': 2.0504708056655868e-05, '"NECAB1"': 2.050129108267139e-05, '"TMX3"': 2.0498680299679558e-05, '"RAVER1"': 2.048960961627672e-05, '"ASB8"': 2.0482591687846293e-05, '"L3MBTL3"': 2.0476491708949163e-05, '"SOX13"': 2.0474626792251806e-05, '"KCNS3"': 2.0461046825388798e-05, '"PFKFB2"': 2.045777002721957e-05, '"SPAG1"': 2.044656616235531e-05, '"SETD9"': 2.0439069721545166e-05, '"TBC1D10A"': 2.043208067022836e-05, '"TMEM250"': 2.043133802183412e-05, '"HOMER2"': 2.042920801182332e-05, '"DRC3"': 2.0418195381351353e-05, '"METTL22"': 2.0410010361311533e-05, '"MOB1B"': 2.039619109053526e-05, '"PHF12"': 2.0392818824814536e-05, '"ACVR1"': 2.0358283453516776e-05, '"CLTB"': 2.0356024400331683e-05, '"CCDC149"': 2.033753352060749e-05, '"MAP3K13"': 2.0322630593933566e-05, '"C12orf56"': 2.031883989965429e-05, '"SERPINE1"': 2.0300087762146666e-05, '"SLC26A4-AS1"': 2.028762673043575e-05, '"TTC39A"': 2.0285390473825538e-05, '"SNHG20"': 2.026244557518813e-05, '"TPGS1"': 2.0260099422875253e-05, '"COA7"': 2.025732402020428e-05, '"NOM1"': 2.025732402020428e-05, '"CDKN1A"': 2.0237425442325388e-05, '"SNAP25-AS1"': 2.022918599520232e-05, '"ZNFX1"': 2.020059502049201e-05, '"ZNF550"': 2.018856630579487e-05, '"UTP18"': 2.0184823745213187e-05, '"ZNF444"': 2.0169152753768693e-05, '"ABHD15"': 2.0153396137593267e-05, '"TRNP1"': 2.0148534211579613e-05, '"LINC01206"': 2.0144378600276257e-05, '"CRB3"': 2.0131654581003236e-05, '"KRT80"': 2.0128910106029806e-05, '"CHAMP1"': 2.0119205901884723e-05, '"S100A16"': 2.0114936866165126e-05, '"DYRK1B"': 2.0114247438412236e-05, '"TMEM259"': 2.0110103357480735e-05, '"ZNF91"': 2.009930498301117e-05, '"C19orf47"': 2.009159524825463e-05, '"PIK3CA"': 2.0078178498159687e-05, '"KRT17"': 2.0073456668873383e-05, '"WDR72"': 2.0053658808722934e-05, '"SNX8"': 2.0019185138459447e-05, '"CDR2L"': 1.9974930683511366e-05, '"SLITRK5"': 1.9939184733670615e-05, '"NTN1"': 1.9915055093991325e-05, '"CLDN11"': 1.991149263261984e-05, '"CBFA2T3"': 1.9889563632811107e-05, '"PTPN9"': 1.9882307797751974e-05, '"NR2F1-AS1"': 1.9878605991178775e-05, '"SULT1B1"': 1.9859538692253403e-05, '"ZBED6"': 1.983070403038489e-05, '"GPBP1"': 1.9809741341134906e-05, '"PKMYT1"': 1.9793941985317523e-05, '"ZNF26"': 1.971918095237796e-05, '"IRAK1"': 1.9697318883350943e-05, '"RAD54L2"': 1.968544003776606e-05, '"CRTC1"': 1.9651161076610775e-05, '"MYO18A"': 1.962899675899507e-05, '"EPOP"': 1.9596822358435895e-05, '"GDPGP1"': 1.9572781283622153e-05, '"PITPNA"': 1.943826051622204e-05, '"DBT"': 1.94147346928935e-05, '"PTPN21"': 1.9387432722231636e-05, '"NCBP3"': 1.9276223991446088e-05, '"GCNT2"': 1.92423637856321e-05, '"SETD2"': 1.9232691747416918e-05, '"TNRC6A"': 1.9227206005518976e-05, '"ZBTB26"': 1.9111392261685885e-05, '"CC2D1A"': 1.904994014777577e-05, '"SRF"': 1.899384320894555e-05, '"NCOA5"': 1.8926748294968284e-05, '"ZNF480"': 1.888638479084275e-05, '"TIAL1"': 1.888638479084275e-05, '"SYCP2"': 1.8824987978371675e-05, '"NSMF"': 1.8814755701506942e-05, '"HIPK2"': 1.8799934760951875e-05, '"RSPH1"': 1.8623807792115273e-05, '"MSMB"': 1.855979014996524e-05, '"CENPE"': 1.8553365591766858e-05, '"RGL2"': 1.8553365591766858e-05, '"SMIM19"': 1.8549791823052095e-05, '"FSBP"': 1.8544500864743344e-05, '"RHBDD2"': 1.852144347610162e-05, '"SMG5"': 1.851146580688877e-05, '"LINC00205"': 1.8506185780312004e-05, '"TTL"': 1.846623645314151e-05, '"CHMP1A"': 1.8178109986516098e-05, '"UGCG"': 1.8174725477649166e-05, '"USP8"': 1.8143454833732203e-05, '"MGAT4B"': 1.81434548337322e-05, '"OPA1"': 1.8142800140738836e-05, '"FGFR1OP2"': 1.8133680790421657e-05, '"RELA"': 1.8133680790421657e-05, '"GDI1"': 1.813368079042165e-05, '"ZCCHC2"': 1.805262525688859e-05, '"NLGN2"': 1.767316248689064e-05, '"ARHGAP12"': 1.767316248689064e-05, '"CACNG4"': 1.7669871992158913e-05, '"CNNM2"': 1.7648426229723446e-05, '"SHOX"': 1.7635657376445562e-05, '"RPL37P6"': 1.7624938838392376e-05, '"PHF1"': 1.7538265021803193e-05, '"FAM131A"': 1.73169147171068e-05, '"IFI27L2"': 1.7026726372375164e-05, '"HEPACAM"': 1.6997746311758476e-05, '"VTI1B"': 1.6997746311758466e-05, '"FAM89A"': 1.696623598741501e-05, '"HSPA4"': 1.696623598741501e-05, '"PABIR2"': 1.6933891178150042e-05, '"RFK"': 1.6924768737726866e-05, '"LINC00294"': 1.6919941284856688e-05, '"CDAN1"': 1.6919941284856678e-05, '"FARP1"': 1.6919941284856678e-05, '"ZNF569"': 1.6883416185729384e-05, '"NFIC"': 1.6883416185729384e-05, '"ANKRD40"': 1.636933780827927e-05, '"HACD4"': 1.6276261831720454e-05, '"HEIH"': 1.593538716727357e-05, '"RPS6KA6"': 1.593538716727357e-05, '"TDRD3"': 1.593538716727357e-05, '"RNF32"': 1.590584623820158e-05, '"CDCA4"': 1.5902884792943022e-05, '"LINC00326"': 1.58835836067511e-05, '"PAPSS2"': 1.5875522979515674e-05, '"RESF1"': 1.5875522979515674e-05, '"SECISBP2L"': 1.5875522979515674e-05, '"ACER3"': 1.5875522979515674e-05, '"FASTK"': 1.5875522979515674e-05, '"MAVS"': 1.5875522979515674e-05, '"ANKRD42"': 1.5872091638801006e-05, '"CLUH"': 1.5862444954553144e-05, '"UAP1L1"': 1.5862444954553144e-05, '"WDR46"': 1.5828202674121296e-05, '"CCP110"': 1.5828202674121296e-05, '"C8orf82"': 1.5513535320040363e-05, '"CYP19A1"': 1.4164788593132063e-05, '"PEA15"': 1.4164788593132063e-05, '"ZNF615"': 1.413589759372713e-05, '"CCDC92"': 1.413589759372713e-05, '"DNAJC25-GNG10"': 1.4118740983778756e-05, '"ELOA"': 1.411157598179171e-05, '"LY6D"': 1.411157598179171e-05, '"C5orf63"': 1.411157598179171e-05, '"ZNF362"': 1.4108525901156449e-05, '"CSRP1"': 1.4103973948105727e-05, '"ISY1"': 1.4103973948105727e-05, '"KCNK6"': 1.4069513488107815e-05, '"YJEFN3"': 1.3858337183929219e-05, '"TENT5C"': 1.3587081550967003e-05, '"PARM1"': 1.338789783914762e-05, '"DYNLL2"': 1.0623591444849047e-05, '"ZHX2"': 1.0623591444849047e-05, '"TMEM94"': 1.0623591444849047e-05, '"PRRC2A"': 1.0603897492134388e-05, '"NR2F6"': 1.0603897492134388e-05, '"PHC3"': 1.0603897492134388e-05, '"TIMELESS"': 1.0589055737834068e-05, '"EFNA5"': 1.0589055737834068e-05, '"KSR2"': 1.0583300082097654e-05, '"ZC3H7A"': 1.0583300082097654e-05, '"JADE2"': 1.0583300082097654e-05, '"CTXN1"': 1.0581394425867338e-05, '"DCTN1"': 1.0581394425867338e-05, '"GSR"': 1.0581394425867338e-05, '"KIF14"': 1.0577980461079298e-05, '"AKR1E2"': 1.0542917959692898e-05, '"INPP4A"': 1.0535767601743573e-05, '"B3GNT6"': 1.052057050601e-05, '"SLC36A2"': 1.0517074962515629e-05, '"PGAP6"': 1.051457735429237e-05, '"HCG11"': 1.0493401349345367e-05, '"CENPB"': 1.0493252181925278e-05, '"ADAP2"': 1.0490710908055937e-05, '"ABTB2"': 1.0482059619155076e-05, '"MMAA"': 1.0471189755113505e-05, '"FAM50A"': 1.0467299502869965e-05, '"KCTD2"': 1.0459680269327798e-05, '"L3MBTL2-AS1"': 1.0438724268812966e-05, '"TF"': 1.0431976066676982e-05, '"KIAA1549"': 1.0414655663912814e-05, '"HSD17B2"': 1.0373316379162745e-05, '"RFNG"': 1.035943206862726e-05, '"CYP1A1"': 1.0358573662728951e-05, '"GNAO1-DT"': 1.0352500364347705e-05, '"HECTD2"': 1.0324626413691519e-05, '"SARS2"': 1.0227648997100954e-05, '"TAT-AS1"': 1.0212922360676904e-05, '"CABLES2"': 9.347077347723714e-06, '"LINC00639"': 9.201391728012679e-06, '"SH2B1"': 8.724667471231497e-06, '"KITLG"': 8.636658410136551e-06, '"KLHL20"': 7.30864904043004e-06, '"LBHD1"': 7.028175934086884e-06, '"USF1"': 7.022543723934502e-06, '"TPH1"': 7.009417260234723e-06, '"OXLD1"': 7.009247659058682e-06, '"HIRIP3"': 6.960862472066059e-06, '"CA4"': 6.947595611179672e-06, '"CEP72"': 6.885240997751393e-06, '"RPL12P25"': 6.842370637185307e-06, '"ZFP41"': 6.784553108184888e-06, '"LATS2"': 6.222501179376955e-06, '"AIMP1P1"': 5.2448854654504145e-06, '"EDEM1"': 5.212674529319776e-06, '"DCP1A"': 5.157732534783956e-06, '"MT-TV"': 4.24167363205372e-06, '"MTCL1"': 4.209504489336642e-06, '"TRPV3"': 4.097524457041883e-06, '"FBXO46"': 4.091521796832076e-06, '"USP38"': 3.59001101266457e-06, '"PEX7"': 2.948001336557594e-06, '"RCC1L"': 2.631686812039102e-06, '"UNC50"': 2.6252348988334453e-06, '"LINC00343"': 2.537372966229962e-06, '"RHOBTB2"': 2.069393703329781e-06, '"HSPA2"': 9.014662668522739e-07, '"SLC35A4"': 6.344116034361867e-07, '"C2orf42"': 0.0, '"DNAI4"': 0.0, '"PCSK5"': 0.0, '"ZNF304"': 0.0, '"PLEKHS1"': 0.0, '"ZDHHC8"': 0.0, '"ZBTB49"': 0.0, '"NKAIN1"': 0.0, '"MTATP6P1"': 0.0, '"RCOR2"': 0.0, '"PAQR4"': 0.0, '"LPAR6"': 0.0, '"SEPTIN3"': 0.0, '"MT-TH"': 0.0, '"NHS"': 0.0, '"ZNF699"': 0.0, '"MT-TM"': 0.0, '"ITM2C"': 0.0, '"MTCO1P40"': 0.0, '"MARS2"': 0.0, '"HPS6"': 0.0, '"ANKRD36BP2"': 0.0, '"TMEM104"': 0.0, '"TIRAP"': 0.0, '"CRAT"': 0.0, '"NPHP4"': 0.0, '"GAS7"': 0.0, '"SLC41A3-AS1"': 0.0, '"GPRASP2"': 0.0, '"ZNF461"': 0.0, '"DOK4"': 0.0, '"MTND2P28"': 0.0, '"ADORA1"': 0.0, '"MPP3"': 0.0, '"ANKRD34A"': 0.0, '"ATG9A"': 0.0, '"LINC00997"': 0.0, '"RAET1E"': 0.0, '"LINC01293"': 0.0, '"MUC5AC"': 0.0, '"ZIC4"': 0.0, '"MT-TT"': 0.0, '"DNAAF8"': 0.0, '"CYP27C1"': 0.0, '"LHX2"': 0.0, '"ZNF573"': 0.0, '"BCL2"': 0.0, '"MT-TY"': 0.0, '"LIMD2"': 0.0, '"MUC5B"': 0.0, '"MARCHF1"': 0.0, '"FOXP3"': 0.0, '"TP53INP2"': 0.0, '"FOXM1"': 0.0, '"MON1A"': 0.0, '"CCDC69"': 0.0, '"SORBS3"': 0.0, '"PDZD2"': 0.0, '"SNORA11F"': 0.0, '"KCTD17"': 0.0, '"ZNF81"': 0.0, '"MSX2"': 0.0, '"PRELID3A"': 0.0, '"CRB1"': 0.0, '"DLG4"': 0.0, '"ATP6V0C"': 0.0, '"LINC01722"': 0.0, '"POC1A"': 0.0, '"RHOQP1"': 0.0, '"PITPNM2"': 0.0, '"FOSL1"': 0.0, '"FANCE"': 0.0, '"PACSIN1"': 0.0, '"C20orf204"': 0.0, '"FAM43A"': 0.0, '"ITPRIP"': 0.0, '"PHETA1"': 0.0, '"ARHGEF26-AS1"': 0.0, '"CORO1A"': 0.0, '"KIF12"': 0.0, '"ZBTB12"': 0.0, '"HHEX"': 0.0, '"SLC22A23"': 0.0, 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'"ABHD8"': 0.0, '"TMPRSS2"': 0.0, '"PPP2R5E"': 0.0, '"GTF2IRD1"': 0.0, '"SH3BP5L"': 0.0, '"GPATCH1"': 0.0, '"FOXP4-AS1"': 0.0, '"GNAQ"': 0.0, '"ATXN7L3"': 0.0, '"AMH"': 0.0, '"HROB"': 0.0, '"MTF1"': 0.0, '"RUNDC1"': 0.0, '"PTAR1"': 0.0, '"GATC"': 0.0, '"DKK1"': 0.0, '"SCRN2"': 0.0, '"MKLN1-AS"': 0.0, '"SYNGAP1"': 0.0, '"TMEM167B-DT"': 0.0, '"TRAM2"': 0.0, '"AK1"': 0.0, '"CAPRIN2"': 0.0, '"WDR90"': 0.0, '"METTL14-DT"': 0.0, '"SUCLA2-AS1"': 0.0, '"FSTL4"': 0.0, '"RFPL3S"': 0.0, '"FNBP1P1"': 0.0, '"DNAJA2"': 0.0, '"LINC02453"': 0.0, '"RCC1"': 0.0, '"STK39"': 0.0, '"MRTFA"': 0.0, '"PIGS"': 0.0, '"PYCR3"': 0.0, '"KCTD20"': 0.0, '"CCNQ"': 0.0, '"PCCA-DT"': 0.0, '"LINC01232"': 0.0, '"ZNF585B"': 0.0, '"LEF1"': 0.0, '"ZNF609"': 0.0, '"RPS12P16"': 0.0, '"PIGB"': 0.0, '"NXPE3"': 0.0, '"LINC00475"': 0.0, '"RETSAT"': 0.0, '"ZNF76"': 0.0, '"AFAP1L2"': 0.0, '"RNF126"': 0.0, '"CHRNG"': 0.0, '"RAB5B"': 0.0, '"CDKN2B"': 0.0, '"LINC00672"': 0.0, '"GNPDA2"': 0.0, '"RALGPS1"': 0.0, '"FUT2"': 0.0, '"RNF220"': 0.0, '"NPLOC4"': 0.0, '"GTPBP6"': 0.0, '"SNAPC5"': 0.0, '"ADARB1"': 0.0, '"TRAF3IP2"': 0.0, '"SAC3D1"': 0.0, '"ZNF8"': 0.0, '"ZNF562"': 0.0, '"WDFY3-AS2"': 0.0, '"DDIAS"': 0.0, '"SF3A2"': 0.0, '"ACTA2"': 0.0, '"STK16"': 0.0, '"CTPS2"': 0.0, '"PPP2R2C"': 0.0, '"SERPINB9P1"': 0.0, '"NANP"': 0.0, '"TPCN2"': 0.0, '"TBCCD1"': 0.0, '"DLX1"': 0.0, '"SATL1"': 0.0, '"PPP2R2B"': 0.0, '"BAHD1"': 0.0, '"SOS2"': 0.0, '"TSPAN17"': 0.0, '"NSMAF"': 0.0, '"ZNF526"': 0.0, '"HNF4A"': 0.0, '"ZNF696"': 0.0, '"FBXW4"': 0.0, '"SERPINB9"': 0.0, '"BBOF1"': 0.0, '"TSSC4"': 0.0, '"SNX4"': 0.0, '"RAI1"': 0.0, '"FCRL5"': 0.0, '"TBXA2R"': 0.0, '"IFFO2"': 0.0, '"OR7E25P"': 0.0, '"RNF44"': 0.0, '"MINK1"': 0.0, '"UBE2QL1"': 0.0, '"EGR3"': 0.0, '"E2F1"': 0.0, '"FER1L5"': 0.0, '"B3GALT5"': 0.0, '"STRIP1"': 0.0, '"ZNF629"': 0.0, '"MFSD4A"': 0.0, '"USP6NL"': 0.0, '"SRP68"': 0.0, '"SCYL3"': 0.0, '"PRR7-AS1"': 0.0, '"MCOLN1"': 0.0, '"PCNX2"': 0.0, '"ZNF324"': 0.0, '"MAPK3"': 0.0, '"BEND7"': 0.0, '"OTUD4"': 0.0, '"ZNF383"': 0.0, '"ENTPD1"': 0.0, '"CDK9"': 0.0, '"MTFR1L"': 0.0, '"EHBP1"': 0.0, '"ATG101"': 0.0, '"CCDC144A"': 0.0, '"SENP5"': 0.0, '"NSRP1P1"': 0.0, '"NPTXR"': 0.0, '"FOXJ2"': 0.0, '"ZNF449"': 0.0, '"RAB30"': 0.0, '"TRAF6"': 0.0, '"PLEKHG1"': 0.0, '"GMEB1"': 0.0, '"C1orf43"': 0.0, '"HLCS"': 0.0, '"EPS8L1"': 0.0, '"BRD7"': 0.0, '"CDKL1"': 0.0, '"TPST1"': 0.0, '"GCM1"': 0.0, '"TADA2B"': 0.0, '"ARHGEF4"': 0.0, '"PROSER3"': 0.0, '"TAF8"': 0.0, '"MIB2"': 0.0, '"ZNF605"': 0.0, '"CHMP6"': 0.0, '"CEP68"': 0.0, '"SIPA1"': 0.0, '"RPL13P2"': 0.0, '"VWA1"': 0.0, '"ZBTB45"': 0.0, '"CCDC71L"': 0.0, '"CTIF"': 0.0, '"STARD3"': 0.0, '"CDK7"': 0.0, '"SLC52A2"': 0.0, '"WFDC1"': 0.0, '"ZNF398"': 0.0, '"KHDC1"': 0.0, '"FRMD8"': 0.0, '"UBA6-DT"': 0.0, '"TPTEP2"': 0.0, '"OR10H1"': 0.0, '"ESCO1"': 0.0, '"PIP4P1"': 0.0, '"DHX37"': 0.0, '"CACNB4"': 0.0, '"VDAC1P8"': 0.0, '"TMPRSS3"': 0.0, '"TMEM212"': 0.0, '"GSDMB"': 0.0, '"MAPK1IP1L"': 0.0, '"ZNF524"': 0.0, '"CIPC"': 0.0, '"RBM14"': 0.0, '"EPAS1"': 0.0, '"CRAMP1"': 0.0, '"PIKFYVE"': 0.0, '"ELAPOR2"': 0.0, '"WDR82"': 0.0, '"LINC00667"': 0.0, '"PYGO1"': 0.0, '"DCLK1"': 0.0, '"MAN2B2"': 0.0, '"INPPL1"': 0.0, '"KRT18P3"': 0.0, '"ZBTB2"': 0.0, '"NAIF1"': 0.0, '"RNF34"': 0.0, '"RGMB"': 0.0, '"STAM-DT"': 0.0, '"SUNO1"': 0.0, '"C22orf46"': 0.0, '"ADAT1"': 0.0, '"SCRG1"': 0.0, '"PDE4A"': 0.0, '"C5orf64"': 0.0, '"USP25"': 0.0, '"ALAD"': 0.0, '"KIAA0753"': 0.0, '"GUCY1A2"': 0.0, '"BCDIN3D"': 0.0, '"MROH1"': 0.0, '"MICALL1"': 0.0, '"RARG"': 0.0, '"BRWD1-AS2"': 0.0, '"AUNIP"': 0.0, '"TNK2"': 0.0}

Apparently, the gene that is more important in determining wether a cell is under hypoxic or normoxic condition is still the TFF1, which wasn't in the first genes in the other analysis.

In [ ]:
# to see the less important ones.
print({k: v for k, v in sorted(genes.items(), key=lambda item: item[1], reverse=False)})
{'"C2orf42"': 0.0, '"DNAI4"': 0.0, '"PCSK5"': 0.0, '"ZNF304"': 0.0, '"PLEKHS1"': 0.0, '"ZDHHC8"': 0.0, '"ZBTB49"': 0.0, '"NKAIN1"': 0.0, '"MTATP6P1"': 0.0, '"RCOR2"': 0.0, '"PAQR4"': 0.0, '"LPAR6"': 0.0, '"SEPTIN3"': 0.0, '"MT-TH"': 0.0, '"NHS"': 0.0, '"ZNF699"': 0.0, '"MT-TM"': 0.0, '"ITM2C"': 0.0, '"MTCO1P40"': 0.0, '"MARS2"': 0.0, '"HPS6"': 0.0, '"ANKRD36BP2"': 0.0, '"TMEM104"': 0.0, '"TIRAP"': 0.0, '"CRAT"': 0.0, '"NPHP4"': 0.0, '"GAS7"': 0.0, '"SLC41A3-AS1"': 0.0, '"GPRASP2"': 0.0, '"ZNF461"': 0.0, '"DOK4"': 0.0, '"MTND2P28"': 0.0, '"ADORA1"': 0.0, '"MPP3"': 0.0, '"ANKRD34A"': 0.0, '"ATG9A"': 0.0, '"LINC00997"': 0.0, '"RAET1E"': 0.0, '"LINC01293"': 0.0, '"MUC5AC"': 0.0, '"ZIC4"': 0.0, '"MT-TT"': 0.0, '"DNAAF8"': 0.0, '"CYP27C1"': 0.0, '"LHX2"': 0.0, '"ZNF573"': 0.0, '"BCL2"': 0.0, '"MT-TY"': 0.0, '"LIMD2"': 0.0, '"MUC5B"': 0.0, '"MARCHF1"': 0.0, '"FOXP3"': 0.0, '"TP53INP2"': 0.0, '"FOXM1"': 0.0, '"MON1A"': 0.0, '"CCDC69"': 0.0, '"SORBS3"': 0.0, '"PDZD2"': 0.0, '"SNORA11F"': 0.0, '"KCTD17"': 0.0, '"ZNF81"': 0.0, '"MSX2"': 0.0, '"PRELID3A"': 0.0, '"CRB1"': 0.0, '"DLG4"': 0.0, '"ATP6V0C"': 0.0, '"LINC01722"': 0.0, '"POC1A"': 0.0, '"RHOQP1"': 0.0, '"PITPNM2"': 0.0, '"FOSL1"': 0.0, '"FANCE"': 0.0, '"PACSIN1"': 0.0, '"C20orf204"': 0.0, '"FAM43A"': 0.0, '"ITPRIP"': 0.0, '"PHETA1"': 0.0, '"ARHGEF26-AS1"': 0.0, '"CORO1A"': 0.0, '"KIF12"': 0.0, '"ZBTB12"': 0.0, '"HHEX"': 0.0, '"SLC22A23"': 0.0, '"DPPA4"': 0.0, '"LAT"': 0.0, '"R3HDM4"': 0.0, '"FOXK1"': 0.0, '"PLEKHA4"': 0.0, '"MAP3K10"': 0.0, '"ALKBH8"': 0.0, '"DDX58"': 0.0, '"PPP1R3B"': 0.0, '"SLC23A2"': 0.0, '"TTYH3"': 0.0, '"SAMD10"': 0.0, '"ERAP2"': 0.0, '"C16orf91"': 0.0, '"ZNF865"': 0.0, '"ARRDC3-AS1"': 0.0, '"CRPPA"': 0.0, '"UCKL1"': 0.0, '"SYNM"': 0.0, '"ZC3H12A"': 0.0, '"DISC1"': 0.0, '"ST3GAL1-DT"': 0.0, '"BRINP2"': 0.0, '"ABCG1"': 0.0, '"ZNF202"': 0.0, '"OPRM1"': 0.0, '"ARRDC2"': 0.0, '"HDAC4"': 0.0, '"ACOT2"': 0.0, '"KCNF1"': 0.0, '"DOCK11"': 0.0, '"ETV6"': 0.0, '"HECTD3"': 0.0, '"LZTR1"': 0.0, '"L3HYPDH"': 0.0, '"SIGLEC15"': 0.0, '"CARF"': 0.0, '"RTL6"': 0.0, '"ZFHX2"': 0.0, '"LMX1B"': 0.0, '"RUSC2"': 0.0, '"RUNDC3A"': 0.0, '"ZNF837"': 0.0, '"LINC01270"': 0.0, '"FAM71D"': 0.0, '"RSAD1"': 0.0, '"ARMC2"': 0.0, '"IRF7"': 0.0, '"RILP"': 0.0, '"HSF2BP"': 0.0, '"KNDC1"': 0.0, '"SLC25A42"': 0.0, '"HAP1"': 0.0, '"CRTC2"': 0.0, '"FAXC"': 0.0, '"LINC00513"': 0.0, '"FRAT1"': 0.0, '"SLC2A11"': 0.0, '"CCDC61"': 0.0, '"ZNF441"': 0.0, '"ERO1B"': 0.0, '"ZNF446"': 0.0, '"FAM185BP"': 0.0, '"CDK8"': 0.0, '"ZNF319"': 0.0, '"CDC42EP3"': 0.0, '"PSEN2"': 0.0, '"CLCN7"': 0.0, '"OXTR"': 0.0, '"ZCCHC14"': 0.0, '"GNRHR2"': 0.0, '"NRARP"': 0.0, '"ZNF324B"': 0.0, '"UCHL1"': 0.0, '"SLC25A22"': 0.0, '"TMCC3"': 0.0, '"PPP1R12A-AS1"': 0.0, '"HSP90AA2P"': 0.0, '"LINC01304"': 0.0, '"LINC01637"': 0.0, '"FBXO6"': 0.0, '"B3GNT7"': 0.0, '"NOVA1"': 0.0, '"SLC45A4"': 0.0, '"DCLRE1A"': 0.0, '"EMX2OS"': 0.0, '"ZNF628"': 0.0, '"SCOC-AS1"': 0.0, '"C8orf58"': 0.0, '"PELI3"': 0.0, '"STX1A"': 0.0, '"FAM241B"': 0.0, '"LRRC20"': 0.0, '"IL1R1"': 0.0, '"DNAJC28"': 0.0, '"LENG8-AS1"': 0.0, '"LINC00240"': 0.0, '"MELTF"': 0.0, '"ZIC5"': 0.0, '"GARNL3"': 0.0, '"TMEM216"': 0.0, '"ROGDI"': 0.0, '"ADAMTSL5"': 0.0, '"PRORSD1P"': 0.0, '"TNS4"': 0.0, '"STOX1"': 0.0, '"WASH6P"': 0.0, '"KATNAL2"': 0.0, '"CARD10"': 0.0, '"OR2L2"': 0.0, '"B4GAT1"': 0.0, '"TBC1D4"': 0.0, '"ZNF433"': 0.0, '"ZNF862"': 0.0, '"SALRNA1"': 0.0, '"CDK18"': 0.0, '"C5AR1"': 0.0, '"ST20-AS1"': 0.0, '"MAS1"': 0.0, '"TIAM1"': 0.0, '"PNMA1"': 0.0, '"BRME1"': 0.0, '"ADAP1"': 0.0, '"LINC02710"': 0.0, '"CLCN6"': 0.0, '"RTN4RL1"': 0.0, '"NCK2"': 0.0, '"PGAP3"': 0.0, '"CAPN5"': 0.0, '"ZNF321P"': 0.0, '"PPP1R18"': 0.0, '"FOXP4"': 0.0, '"CTSK"': 0.0, '"MOGAT3"': 0.0, '"SRC"': 0.0, '"SHISA4"': 0.0, '"PACC1"': 0.0, '"B3GNT5"': 0.0, '"FOSB"': 0.0, '"MAPK12"': 0.0, '"ZEB1-AS1"': 0.0, '"MEMO1"': 0.0, '"FRAS1"': 0.0, '"SLC4A10"': 0.0, '"HGH1"': 0.0, '"TMEM184B"': 0.0, '"AP1M1"': 0.0, '"ZNF816"': 0.0, '"FAM72D"': 0.0, '"GADD45A"': 0.0, '"DPY19L2P1"': 0.0, '"FGFR2"': 0.0, '"PDZRN3"': 0.0, '"BMS1P22"': 0.0, '"MYLPF"': 0.0, '"ATG16L2"': 0.0, '"RBM24"': 0.0, '"EML6"': 0.0, '"RHNO1"': 0.0, '"COLCA1"': 0.0, '"ZNF79"': 0.0, '"RBM26-AS1"': 0.0, '"SLC19A2"': 0.0, '"SIGMAR1"': 0.0, '"PCDHA10"': 0.0, '"VPS18"': 0.0, '"ZCCHC24"': 0.0, '"ESRRA"': 0.0, '"DENND6B"': 0.0, '"IGHMBP2"': 0.0, '"CCDC88A"': 0.0, '"SKI"': 0.0, '"TET3"': 0.0, '"LINC01214"': 0.0, '"CDKN2D"': 0.0, '"CAB39L"': 0.0, '"GREM1"': 0.0, '"KIZ"': 0.0, '"RNF146"': 0.0, '"PLEKHG6"': 0.0, '"SCAMP5"': 0.0, '"PCDHB9"': 0.0, '"CHAC2"': 0.0, '"CRYBG2"': 0.0, '"PODNL1"': 0.0, '"ATXN2L"': 0.0, '"ZNF30"': 0.0, '"GYS1"': 0.0, '"NPRL3"': 0.0, '"KLHL21"': 0.0, '"SYT16"': 0.0, '"RAPGEFL1"': 0.0, '"PURPL"': 0.0, '"OR10K1"': 0.0, '"CROCCP3"': 0.0, '"HMGA2"': 0.0, '"LINC02762"': 0.0, '"CATSPER2"': 0.0, '"ZNF722P"': 0.0, '"MHENCR"': 0.0, '"POLM"': 0.0, '"RTL10"': 0.0, '"LRRC69"': 0.0, '"PKN2-AS1"': 0.0, '"CLYBL"': 0.0, '"DGKQ"': 0.0, '"PAX5"': 0.0, '"PCDH11X"': 0.0, '"CATSPERB"': 0.0, '"KDM7A-DT"': 0.0, '"EPS15-AS1"': 0.0, '"TRIM8"': 0.0, '"KIAA0895"': 0.0, '"RPL10AP6"': 0.0, '"RNF157"': 0.0, '"HCN2"': 0.0, '"MIRLET7BHG"': 0.0, '"FHIP1A"': 0.0, '"CDKL3"': 0.0, '"ADCK1"': 0.0, '"CERS2"': 0.0, '"ROM1"': 0.0, '"GPR158"': 0.0, '"PHLDA1"': 0.0, '"OLFM2"': 0.0, '"LRRC73"': 0.0, '"RNF19B"': 0.0, '"SREK1IP1P1"': 0.0, '"TRMT61B"': 0.0, '"USP7-AS1"': 0.0, '"CDC14A"': 0.0, '"GRIN1"': 0.0, '"SCN9A"': 0.0, '"ARMC7"': 0.0, '"ZDHHC18"': 0.0, '"TRIM66"': 0.0, '"RPL23AP53"': 0.0, '"C1orf210"': 0.0, '"IPO8P1"': 0.0, '"STON2"': 0.0, '"LIX1L"': 0.0, '"ZNF674-AS1"': 0.0, '"TMEM169"': 0.0, '"KIAA0825"': 0.0, '"FAM86C2P"': 0.0, '"ZNF436"': 0.0, '"PA2G4P6"': 0.0, '"C6orf136"': 0.0, '"EHHADH"': 0.0, '"DISP1"': 0.0, '"GCAWKR"': 0.0, '"ZSWIM5"': 0.0, '"SGMS1-AS1"': 0.0, '"DLGAP1-AS2"': 0.0, '"TCF20"': 0.0, '"KLK10"': 0.0, '"SYNPO2L"': 0.0, '"EML5"': 0.0, '"MUL1"': 0.0, '"IFIT5"': 0.0, '"ZNF286B"': 0.0, '"SNHG11"': 0.0, '"ARHGEF18"': 0.0, '"MANBAL"': 0.0, '"HELQ"': 0.0, '"SLC46A1"': 0.0, '"FGD3"': 0.0, '"LINC02241"': 0.0, '"ZNF385A"': 0.0, '"FJX1"': 0.0, '"ZNF69"': 0.0, '"MYB"': 0.0, '"TP53INP1"': 0.0, '"FAM171A2"': 0.0, '"SPHK1"': 0.0, '"EDA2R"': 0.0, '"SGSH"': 0.0, '"GMIP"': 0.0, '"STK40"': 0.0, '"CREB3L1"': 0.0, '"RAB4B"': 0.0, '"TBC1D8"': 0.0, '"RAB29"': 0.0, '"GBP1P1"': 0.0, '"NARF-AS2"': 0.0, '"LINC00863"': 0.0, '"LINC01963"': 0.0, '"INCENP"': 0.0, '"PLCG2"': 0.0, '"PLEKHG5"': 0.0, '"ZFYVE28"': 0.0, '"PLCD4"': 0.0, '"ZIC1"': 0.0, '"LINC01234"': 0.0, '"TRPT1"': 0.0, '"ZBTB34"': 0.0, '"CTU2"': 0.0, '"ATRNL1"': 0.0, '"ZNF391"': 0.0, '"PCDHGA2"': 0.0, '"METTL7A"': 0.0, '"NDRG4"': 0.0, '"SCX"': 0.0, '"CAMTA2"': 0.0, '"CALHM2"': 0.0, '"RBFOX3"': 0.0, '"LRRC56"': 0.0, '"MAFK"': 0.0, '"ZMAT3"': 0.0, '"NLRC3"': 0.0, '"LYPLA2"': 0.0, '"GPR153"': 0.0, '"PARS2"': 0.0, '"ADRA2C"': 0.0, '"SENP3"': 0.0, '"KCNJ2"': 0.0, '"C11orf71"': 0.0, '"CERK"': 0.0, '"ZKSCAN2"': 0.0, '"GLB1L"': 0.0, '"LENG9"': 0.0, '"CCNC"': 0.0, '"H2AC10P"': 0.0, '"ANKRD13B"': 0.0, '"HDHD5-AS1"': 0.0, '"CEP170B"': 0.0, '"DOCK9"': 0.0, '"RIPOR2"': 0.0, '"FGFBP3"': 0.0, '"A4GALT"': 0.0, '"BMP8A"': 0.0, '"MAPT-AS1"': 0.0, '"LINC01962"': 0.0, '"KCNJ15"': 0.0, '"PCAT19"': 0.0, '"S100A8"': 0.0, '"PYCR2"': 0.0, '"TMEM51"': 0.0, '"TRABD2A"': 0.0, '"TNFAIP8L3"': 0.0, '"MPPED2"': 0.0, '"ASH1L-AS1"': 0.0, '"SCNN1A"': 0.0, '"LINC02482"': 0.0, '"ALDH3B2"': 0.0, '"ARHGEF19"': 0.0, '"PIDD1"': 0.0, '"FUOM"': 0.0, '"PSMC1P10"': 0.0, '"RNU6-450P"': 0.0, '"STAMBPL1"': 0.0, '"GRM6"': 0.0, '"SNN"': 0.0, '"AP1G1"': 0.0, '"HOMER3"': 0.0, '"TAF3"': 0.0, '"HIF3A"': 0.0, '"HR"': 0.0, '"ATP2A1-AS1"': 0.0, '"SIMC1"': 0.0, '"INMT"': 0.0, '"GMFB"': 0.0, '"UNC5B"': 0.0, '"EFNA2"': 0.0, '"IKZF4"': 0.0, '"ABR"': 0.0, '"ZNF571-AS1"': 0.0, '"PABPC1L"': 0.0, '"PCF11"': 0.0, '"SUSD3"': 0.0, '"SAMD4B"': 0.0, '"MCM2"': 0.0, '"HARBI1"': 0.0, '"CHST6"': 0.0, '"TRIM69"': 0.0, '"SNX24"': 0.0, '"CDC42EP1"': 0.0, '"ZNF396"': 0.0, '"SNX27"': 0.0, '"EMP3"': 0.0, '"MYO9B"': 0.0, '"PLEKHH3"': 0.0, '"EPM2A"': 0.0, '"ZFP3"': 0.0, '"BICRAL"': 0.0, '"YTHDF3"': 0.0, '"INAFM2"': 0.0, '"XKR6"': 0.0, '"VPS13B-DT"': 0.0, '"LRP3"': 0.0, '"CEP85"': 0.0, '"KIF26A"': 0.0, '"S100A2"': 0.0, '"AGAP3"': 0.0, '"RAB40C"': 0.0, '"ITGB6"': 0.0, '"LIFR"': 0.0, '"ZNF354C"': 0.0, '"CPSF4"': 0.0, '"CLCF1"': 0.0, '"CRACR2B"': 0.0, '"DLG5-AS1"': 0.0, '"TSBP1-AS1"': 0.0, '"NES"': 0.0, '"PARD3B"': 0.0, '"PTPN7"': 0.0, '"VASN"': 0.0, '"VEPH1"': 0.0, '"THAP1"': 0.0, '"ERF"': 0.0, '"CCDC18-AS1"': 0.0, '"LINC01355"': 0.0, '"TNFRSF10B"': 0.0, '"TUBG2"': 0.0, '"CEP162"': 0.0, '"DNM3"': 0.0, '"SLC19A1"': 0.0, '"STRIT1"': 0.0, '"CAPN10-DT"': 0.0, '"LINC00352"': 0.0, '"PPP2R3B"': 0.0, '"CNR2"': 0.0, '"BACH2"': 0.0, '"CARM1"': 0.0, '"SMPD2"': 0.0, '"GYG2"': 0.0, '"PML"': 0.0, '"ZYX"': 0.0, '"DENND3"': 0.0, '"CCDC102A"': 0.0, '"RHD"': 0.0, '"TRAK2"': 0.0, '"TJP3"': 0.0, '"HMGB1P8"': 0.0, '"LINC01128"': 0.0, '"LINC00853"': 0.0, '"SLC52A3"': 0.0, '"HDAC7"': 0.0, '"NOG"': 0.0, '"C3orf62"': 0.0, '"MAP7D1"': 0.0, '"NXN"': 0.0, '"ZNF672"': 0.0, '"PIP5K1C"': 0.0, '"C9orf152"': 0.0, 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1.8814755701506942e-05, '"SYCP2"': 1.8824987978371675e-05, '"ZNF480"': 1.888638479084275e-05, '"TIAL1"': 1.888638479084275e-05, '"NCOA5"': 1.8926748294968284e-05, '"SRF"': 1.899384320894555e-05, '"CC2D1A"': 1.904994014777577e-05, '"ZBTB26"': 1.9111392261685885e-05, '"TNRC6A"': 1.9227206005518976e-05, '"SETD2"': 1.9232691747416918e-05, '"GCNT2"': 1.92423637856321e-05, '"NCBP3"': 1.9276223991446088e-05, '"PTPN21"': 1.9387432722231636e-05, '"DBT"': 1.94147346928935e-05, '"PITPNA"': 1.943826051622204e-05, '"GDPGP1"': 1.9572781283622153e-05, '"EPOP"': 1.9596822358435895e-05, '"MYO18A"': 1.962899675899507e-05, '"CRTC1"': 1.9651161076610775e-05, '"RAD54L2"': 1.968544003776606e-05, '"IRAK1"': 1.9697318883350943e-05, '"ZNF26"': 1.971918095237796e-05, '"PKMYT1"': 1.9793941985317523e-05, '"GPBP1"': 1.9809741341134906e-05, '"ZBED6"': 1.983070403038489e-05, '"SULT1B1"': 1.9859538692253403e-05, '"NR2F1-AS1"': 1.9878605991178775e-05, '"PTPN9"': 1.9882307797751974e-05, '"CBFA2T3"': 1.9889563632811107e-05, '"CLDN11"': 1.991149263261984e-05, '"NTN1"': 1.9915055093991325e-05, '"SLITRK5"': 1.9939184733670615e-05, '"CDR2L"': 1.9974930683511366e-05, '"SNX8"': 2.0019185138459447e-05, '"WDR72"': 2.0053658808722934e-05, '"KRT17"': 2.0073456668873383e-05, '"PIK3CA"': 2.0078178498159687e-05, '"C19orf47"': 2.009159524825463e-05, '"ZNF91"': 2.009930498301117e-05, '"TMEM259"': 2.0110103357480735e-05, '"DYRK1B"': 2.0114247438412236e-05, '"S100A16"': 2.0114936866165126e-05, '"CHAMP1"': 2.0119205901884723e-05, '"KRT80"': 2.0128910106029806e-05, '"CRB3"': 2.0131654581003236e-05, '"LINC01206"': 2.0144378600276257e-05, '"TRNP1"': 2.0148534211579613e-05, '"ABHD15"': 2.0153396137593267e-05, '"ZNF444"': 2.0169152753768693e-05, '"UTP18"': 2.0184823745213187e-05, '"ZNF550"': 2.018856630579487e-05, '"ZNFX1"': 2.020059502049201e-05, '"SNAP25-AS1"': 2.022918599520232e-05, '"CDKN1A"': 2.0237425442325388e-05, '"COA7"': 2.025732402020428e-05, '"NOM1"': 2.025732402020428e-05, '"TPGS1"': 2.0260099422875253e-05, '"SNHG20"': 2.026244557518813e-05, '"TTC39A"': 2.0285390473825538e-05, '"SLC26A4-AS1"': 2.028762673043575e-05, '"SERPINE1"': 2.0300087762146666e-05, '"C12orf56"': 2.031883989965429e-05, '"MAP3K13"': 2.0322630593933566e-05, '"CCDC149"': 2.033753352060749e-05, '"CLTB"': 2.0356024400331683e-05, '"ACVR1"': 2.0358283453516776e-05, '"PHF12"': 2.0392818824814536e-05, '"MOB1B"': 2.039619109053526e-05, '"METTL22"': 2.0410010361311533e-05, '"DRC3"': 2.0418195381351353e-05, '"HOMER2"': 2.042920801182332e-05, '"TMEM250"': 2.043133802183412e-05, '"TBC1D10A"': 2.043208067022836e-05, '"SETD9"': 2.0439069721545166e-05, '"SPAG1"': 2.044656616235531e-05, '"PFKFB2"': 2.045777002721957e-05, '"KCNS3"': 2.0461046825388798e-05, '"SOX13"': 2.0474626792251806e-05, '"L3MBTL3"': 2.0476491708949163e-05, '"ASB8"': 2.0482591687846293e-05, '"RAVER1"': 2.048960961627672e-05, '"TMX3"': 2.0498680299679558e-05, '"NECAB1"': 2.050129108267139e-05, '"SACS"': 2.0504708056655868e-05, '"L2HGDH"': 2.0505143909064208e-05, '"VPS52"': 2.0513279278500714e-05, '"VASH1"': 2.0560172569767022e-05, '"RPLP0P2"': 2.0560807760890073e-05, '"UBP1"': 2.0561220268631438e-05, '"SDCBP2-AS1"': 2.05799753180846e-05, '"ZNF154"': 2.0583169818704647e-05, '"BAG1"': 2.058403630826087e-05, '"CSKMT"': 2.0585910869464883e-05, '"TMCO6"': 2.0589531933816316e-05, '"WNK1"': 2.058953193381637e-05, '"GMCL1"': 2.059527305450682e-05, '"ARHGAP39"': 2.059693292301483e-05, '"PRR12"': 2.059770382596343e-05, '"ZNF326"': 2.0598984778230372e-05, '"CASP10"': 2.0601135844070366e-05, '"ANKRD20A5P"': 2.060264641603972e-05, '"MAP3K14-AS1"': 2.060460962648021e-05, '"DUS4L"': 2.0614850657518732e-05, '"GPR132"': 2.0617462028476732e-05, '"TEDC2-AS1"': 2.0635286449224795e-05, '"ABHD3"': 2.06354844966806e-05, '"KIFC2"': 2.0640141460434965e-05, '"FBRSL1"': 2.0640155327914795e-05, '"BRPF3"': 2.0646356924973933e-05, '"ARL17B"': 2.0648320714905126e-05, '"SCMH1"': 2.0650596532194132e-05, '"ZADH2"': 2.0659621128223297e-05, '"CTNS"': 2.06602601516309e-05, '"FMNL3"': 2.0663776044790453e-05, '"BRF1"': 2.0663885716522327e-05, '"ZNF879"': 2.0667782698220923e-05, '"ACTR5"': 2.067375023082593e-05, '"NAA16"': 2.0675190010317052e-05, '"RBM15B"': 2.0682752992387867e-05, '"LINC01291"': 2.0692454802909053e-05, '"KIF9-AS1"': 2.069473880765379e-05, '"PSMF1"': 2.069657318605929e-05, '"PCDHGB6"': 2.0698934712987065e-05, '"RASAL1"': 2.0699633578294426e-05, '"DTYMK"': 2.0709303135111052e-05, '"EN2"': 2.0709689059681033e-05, '"NDUFA6-DT"': 2.0710201621106356e-05, '"ZNF512"': 2.071089093316712e-05, '"MAPKAPK5"': 2.0717717747936255e-05, '"OGN"': 2.071985645431565e-05, '"PIP4K2A"': 2.072194079080454e-05, '"NEK8"': 2.072577121497048e-05, '"LINC01725"': 2.0726163240855794e-05, '"GTPBP2"': 2.0732428891944286e-05, '"OTUB2"': 2.0741410747558938e-05, '"DIABLO"': 2.0741897996440507e-05, '"IPO5P1"': 2.0742468802751938e-05, '"FOXK2"': 2.074537684513541e-05, '"ZNF254"': 2.0746844690215974e-05, '"KLHL22"': 2.074754406866178e-05, '"PCDHB4"': 2.075687347574915e-05, '"F8"': 2.0760668617492763e-05, '"FMN1"': 2.0761465104747515e-05, '"PLCB1"': 2.0763106623607375e-05, '"FBXO27"': 2.076534900426496e-05, '"MMP25-AS1"': 2.0766878586764208e-05, '"CDK12"': 2.077245086672717e-05, '"TPPP3"': 2.0774626087080578e-05, '"HMGN1P14"': 2.077601459316964e-05, '"PRMT6"': 2.0776678252577653e-05, '"TP53BP2"': 2.0779602813759645e-05, '"SHISA2"': 2.0780987894753832e-05, '"GRIPAP1"': 2.0784476064994202e-05, '"SLC36A4"': 2.0794031761655143e-05, '"DUSP7"': 2.079413762749336e-05, '"LINC00844"': 2.0796320803405252e-05, '"KMT2B"': 2.080547014098906e-05, '"GAREM1"': 2.080623211473077e-05, '"B9D1"': 2.080721049288026e-05, '"PPT2"': 2.0809648740482917e-05, '"MAP2K5"': 2.0814769255592027e-05, '"YRDC"': 2.081585788695214e-05, '"HES6"': 2.081834270293025e-05, '"SLC43A2"': 2.0820592412347e-05, '"NAT8L"': 2.0821489749807745e-05, '"THEM4"': 2.0826087262503284e-05, '"BAGE2"': 2.0826955453490343e-05, '"CCNT2-AS1"': 2.0831385193264815e-05, '"CCM2"': 2.0831842957580174e-05, '"TMEM115"': 2.083407157655607e-05, '"FBXO30"': 2.0838262832132234e-05, '"GSE1"': 2.0838583218742363e-05, '"KCTD18"': 2.0842807435925668e-05, '"MED25"': 2.0850496130166625e-05, '"AFF4"': 2.0851433167125064e-05, '"CLEC16A"': 2.0856878988835095e-05, '"WIPI2"': 2.0859903523642346e-05, '"KYAT3"': 2.086564836707798e-05, '"AQP11"': 2.0865733774845014e-05, '"NBEAL2"': 2.0866668659849488e-05, '"RC3H2"': 2.0867768909524927e-05, '"RADIL"': 2.0870824420730917e-05, '"FGF12"': 2.0871494352025445e-05, '"TUT4"': 2.0872012124005314e-05, '"EPHB4"': 2.0877804293886503e-05, '"IGDCC3"': 2.088047720922826e-05, '"OR9H1P"': 2.0889165529881326e-05, '"IRS3P"': 2.0889599558414017e-05, '"FN3K"': 2.0891260730772364e-05, '"NOP2"': 2.0891709252971997e-05, '"LIAS"': 2.0893467047586364e-05, '"LCORL"': 2.0904706060859862e-05, '"CAMKK2"': 2.0905200666779556e-05, '"CALR4P"': 2.0907815492075294e-05, '"ZNF579"': 2.0909586531001877e-05, '"MT-TP"': 2.091433587874354e-05, '"SENP7"': 2.091583924794596e-05, '"TRIM14"': 2.0916083629108834e-05, '"ABLIM1"': 2.0917057267696935e-05, '"CCNY-AS1"': 2.091942932228465e-05, '"ESRP2"': 2.09234394932872e-05, '"HMGB1P51"': 2.092453363008472e-05, '"CDH6"': 2.0926004825178782e-05, '"SIX4"': 2.0926117858917117e-05, '"DPY19L1P1"': 2.0926548384984005e-05, '"SLC25A25-AS1"': 2.0929154815219718e-05, '"ABCC4"': 2.0929604893957845e-05, '"ABHD1"': 2.0930820330986274e-05, '"HELZ2"': 2.0932190613561616e-05, '"KMT2D"': 2.0934533070479004e-05, '"MMD"': 2.0934684906982295e-05, '"ORAI1"': 2.0935972709187955e-05, '"NCOA2"': 2.0936532033571205e-05, '"ATP1A4"': 2.093675441068902e-05, '"TBC1D9"': 2.0937283929506354e-05, '"BRMS1L"': 2.0938743563113223e-05, '"CERS4"': 2.0941439836069775e-05, '"RFFL"': 2.094155236422879e-05, '"TMEM222"': 2.0941570235338585e-05, '"TCHH"': 2.0942070509225395e-05, '"PCAT1"': 2.0942800998892587e-05, '"ELP3"': 2.0943090714971385e-05, '"SMIM5"': 2.0945069988088533e-05, '"ZZEF1"': 2.0945491006926852e-05, '"MGLL"': 2.0949394553416738e-05, '"FAM189B"': 2.0950751873514164e-05, '"MAN1C1"': 2.0951562140009373e-05, '"ERVK13-1"': 2.095587177496366e-05, '"ITSN1"': 2.0957020390249198e-05, '"PTPN13"': 2.0959578031836385e-05, '"NAGLU"': 2.095994652072809e-05, '"RPL12P38"': 2.0961512564308405e-05, '"FAM20C"': 2.0962683736107358e-05, '"MYO3B-AS1"': 2.0963457829931104e-05, '"PSMD13"': 2.0963634004684424e-05, '"MC2R"': 2.0964432058991023e-05, '"SRFBP1"': 2.0965005778353975e-05, '"PATZ1"': 2.096679731399293e-05, '"FAM86EP"': 2.0969343567247435e-05, '"LPCAT4"': 2.0970268095751868e-05, '"NPTN"': 2.0972498742894682e-05, '"CYB561D2"': 2.0974847941534434e-05, '"NEUROD2"': 2.0975148491999175e-05, '"ULK3"': 2.097543528039283e-05, '"TMEM80"': 2.097610152854098e-05, '"VPS9D1-AS1"': 2.0979407533187898e-05, '"VPS54"': 2.0982085577624848e-05, '"DUSP8"': 2.0984069109925777e-05, '"RHOU"': 2.0984548363481343e-05, '"NLK"': 2.0987687286981888e-05, '"CEP63"': 2.0987979532241063e-05, '"APOBEC3F"': 2.099357109711859e-05, '"PPOX"': 2.099568849093021e-05, '"ZNF777"': 2.0999764750173554e-05, '"GCAT"': 2.1001993941650943e-05, '"VAT1"': 2.1002119371547677e-05, '"ACKR3"': 2.1004678928663263e-05, '"IER5L"': 2.1004689443868106e-05, '"POTEC"': 2.100581598441841e-05, '"NFATC2"': 2.100621351977524e-05, '"ANKH"': 2.100841156077055e-05, '"DCAF10"': 2.1009398569906258e-05, '"GPN1"': 2.10097627518752e-05, '"TXNRD2"': 2.1011354692395086e-05, '"ABL1"': 2.1015649033304143e-05, '"RNF180"': 2.1017777321374008e-05, '"ZNF134"': 2.1018877554798446e-05, '"CDC42BPA"': 2.1025489496434007e-05, '"FAM104A"': 2.102551527309377e-05, '"KCNJ6"': 2.1027037042564393e-05, '"ARID4B"': 2.1030991516077698e-05, '"TNS2"': 2.103154437940148e-05, '"NUP98"': 2.1032242006113392e-05, '"INPP5E"': 2.1032507135563108e-05, '"AFF1"': 2.1034042690119373e-05, '"DEAF1"': 2.103505169699975e-05, '"PHACTR1"': 2.103669099083971e-05, '"MAP3K12"': 2.1036802818495805e-05, '"MT-TL1"': 2.1041136178658526e-05, '"DCAF4"': 2.104288305422023e-05, '"JMJD8"': 2.1047067743561676e-05, '"SYT14"': 2.1049657621851686e-05, '"ZNF620"': 2.105416951294066e-05, '"ALDH4A1"': 2.105668905525349e-05, '"TM4SF19-AS1"': 2.1061066136423937e-05, '"ZNF626"': 2.106111221532704e-05, '"PLCB4"': 2.106126172880751e-05, '"FAAP100"': 2.1070403544816334e-05, '"MEX3D"': 2.107077699297614e-05, '"ZNF121"': 2.107813769632773e-05, '"SALL4"': 2.1080137357859023e-05, '"TRMT2A"': 2.1080582584411277e-05, '"TMEM164"': 2.1082246772603578e-05, '"AVEN"': 2.1083772791378315e-05, '"PARVB"': 2.1086179267272994e-05, '"LINC00173"': 2.1087207462978478e-05, '"GPR85"': 2.1090186445190995e-05, '"TSPAN33"': 2.109437306243696e-05, '"CNOT6L"': 2.110486629936818e-05, '"DENND1B"': 2.1105834431459793e-05, '"ZNF772"': 2.11075489155453e-05, '"STX2"': 2.1111253174911257e-05, '"SLC4A11"': 2.1119247074663946e-05, '"TRERF1"': 2.1125603414979657e-05, '"GPATCH3"': 2.1127816693688747e-05, '"NKIRAS2"': 2.1128009583681144e-05, '"PANK4"': 2.1131552874328338e-05, '"VDR"': 2.1135224820002353e-05, '"TGFB3"': 2.1146504278664372e-05, '"CNDP2"': 2.1147166106301412e-05, '"REST"': 2.115921116735739e-05, '"TEPSIN"': 2.116226821251515e-05, '"KLC2"': 2.1175401866422114e-05, '"ZNF232"': 2.1177604006443596e-05, '"TRIP13"': 2.1180577300702177e-05, '"NUP62"': 2.1207794984268775e-05, '"PHKG2"': 2.175463473113577e-05, '"PTPDC1"': 2.20564384183771e-05, '"CPEB4"': 2.2216093803650572e-05, '"ZNF442"': 2.333158098836578e-05, '"FLVCR2"': 2.3921200820812403e-05, '"CSK"': 2.417134469265241e-05, '"TMEM178B"': 2.47533755736443e-05, '"PCGF2"': 2.4838077881736066e-05, '"PLAGL1"': 2.5275244010494252e-05, '"SCRIB"': 2.5387153106590312e-05, '"KIF3B"': 2.541373377080176e-05, '"EDA"': 2.6133294806911026e-05, '"BOP1"': 2.615861226215584e-05, '"TTLL12"': 2.6162263720678197e-05, '"DOCK8-AS1"': 2.6370677204777762e-05, '"FBXO11"': 2.6474472235843126e-05, '"OTULIN"': 2.6738815971026563e-05, '"JPH3"': 2.6824673828710097e-05, '"APOOL"': 2.6879263303687306e-05, '"GYG1"': 2.7076016616124983e-05, '"IFI27"': 2.73261215826236e-05, '"ZNF572"': 2.741513349653836e-05, '"GCNA"': 2.7464134905785622e-05, '"SOX7"': 2.7529355747907695e-05, '"CCNYL1"': 2.7540180160804092e-05, '"TRIM41"': 2.7685789313721683e-05, '"ZDHHC7"': 2.780130499915894e-05, '"ULK1"': 2.7973311326386642e-05, '"KLHL7"': 2.813902697621563e-05, '"GCC2"': 2.827179518745426e-05, '"RAB35"': 2.838059629967166e-05, '"SLC35C1"': 2.8564617313909615e-05, '"LCMT1"': 2.902466498419912e-05, '"NETO2"': 2.9101241276813864e-05, '"POLB"': 2.9394354335308372e-05, '"CCNO"': 2.968781753187504e-05, '"FAM219B"': 3.0156180558462954e-05, '"R3HDM2"': 3.0214180865815508e-05, '"ATMIN"': 3.0232555502478104e-05, '"TIGAR"': 3.0393591095042994e-05, '"DTX3"': 3.0501849656378872e-05, '"EEA1"': 3.0510320673472837e-05, '"CMSS1"': 3.0549323727339554e-05, '"CALML3-AS1"': 3.094076195311798e-05, '"PAK4"': 3.1247643817289385e-05, '"LINC01278"': 3.128697784333444e-05, '"CMPK1"': 3.1440774343037374e-05, '"MTMR12"': 3.173394138323789e-05, '"RGPD4-AS1"': 3.174990024629296e-05, '"MAD2L1BP"': 3.187426774102608e-05, '"ZMYM3"': 3.246889569375728e-05, '"BCL2L15"': 3.260178679934653e-05, '"MAPK8IP2"': 3.2684848597791694e-05, '"CRK"': 3.306359567744544e-05, '"UQCC3"': 3.376246597350026e-05, '"RNF168"': 3.408701350860271e-05, '"C11orf24"': 3.415144391378255e-05, '"SEPTIN9"': 3.416121443262958e-05, '"PATJ"': 3.4239143464934616e-05, '"BICD2"': 3.4343938177059395e-05, '"ITGB8-AS1"': 3.438804838533191e-05, '"SAPCD2"': 3.4389769387063105e-05, '"DNAJC5"': 3.443189828629751e-05, '"SAMD12"': 3.456697684652928e-05, '"CAMK2N1"': 3.461884514535043e-05, '"ZNF510"': 3.479248840113535e-05, '"RIC8A"': 3.4958445639811775e-05, '"DOHH"': 3.503505381689361e-05, '"FAM120A"': 3.521973506620912e-05, '"SNAPC2"': 3.5277666940325505e-05, '"AHCYL1"': 3.541040499650153e-05, '"KIAA1522"': 3.5556638571903576e-05, '"ERVK3-1"': 3.564335291473761e-05, '"TPCN1"': 3.568006366331317e-05, '"TAF13"': 3.587426153960223e-05, '"KCNG1"': 3.623676676807386e-05, '"VRK3"': 3.626163214270277e-05, '"ETNK1"': 3.62822178671456e-05, '"BDP1"': 3.6356219973032196e-05, '"SLC24A2"': 3.6594541443651655e-05, '"PRPS1"': 3.677854484471193e-05, '"DCTN5"': 3.685370060652758e-05, '"ELOVL7"': 3.698979147423084e-05, '"MAEA"': 3.712372203757839e-05, '"PTBP3"': 3.75756852684609e-05, '"ALDH2"': 3.7668165846212834e-05, '"DNAJA3"': 3.780284959214709e-05, '"FAM222B"': 3.789350876676902e-05, '"PICALM"': 3.7953916826993394e-05, '"RRAGC"': 3.80212746447229e-05, '"LPP"': 3.8051054045982735e-05, '"POLD2"': 3.809988029555155e-05, '"VCPIP1"': 3.812311663311038e-05, '"EIF4G3"': 3.81305250435675e-05, '"SMC6"': 3.832089723039311e-05, '"MICAL2"': 3.836901894804629e-05, '"POGK"': 3.8466596678964945e-05, '"C5"': 3.8482612675320215e-05, '"SLC66A2"': 3.848472757126422e-05, '"RASGEF1B"': 3.863124161763292e-05, '"SLC25A43"': 3.870168469653623e-05, '"RRP15"': 3.872793060354155e-05, '"MAPK9"': 3.8808128643291615e-05, '"PHLDA2"': 3.881062038786274e-05, '"PLD6"': 3.884944411903769e-05, '"CEP83"': 3.894817764400047e-05, '"GAB2"': 3.901507735868688e-05, '"CHD8"': 3.903379263227481e-05, '"DCTN6-DT"': 3.909481651704449e-05, '"FBXL4"': 3.914437684356535e-05, '"GOLGA5"': 3.9170470691136254e-05, '"PSMC5"': 3.921872495494099e-05, '"KCTD15"': 3.924070898611251e-05, '"F3"': 3.9317707859485304e-05, '"XRCC2"': 3.9323040745102485e-05, '"YJU2"': 3.9323762679152536e-05, '"FMR1"': 3.933804503612847e-05, '"SSH3"': 3.950257127797192e-05, '"SCARA3"': 3.950441748503334e-05, '"EPS8L2"': 3.954470052041709e-05, '"CXADR"': 3.95741904791198e-05, '"MYADM"': 3.9584173859579076e-05, '"TESK1"': 3.9592699381051244e-05, '"SENP6"': 3.969930916561688e-05, '"RECQL4"': 3.9734587918233305e-05, '"MTMR2"': 3.973563146844003e-05, '"WDR5"': 3.975667336559496e-05, '"CLSPN"': 3.980947730778672e-05, '"GLE1"': 3.98787601748766e-05, '"RALBP1"': 3.991844654100849e-05, '"ZNRF1"': 3.9923334473310204e-05, '"MIR4458HG"': 3.993251993045276e-05, '"ERVMER34-1"': 3.99456169374027e-05, '"GUCY1B2"': 4.00006384483388e-05, '"FBXL19"': 4.006718155090569e-05, '"LYPD6"': 4.007467795692191e-05, '"MOB2"': 4.007594425840817e-05, '"ZNF329"': 4.0092165662316955e-05, '"CRYL1"': 4.0198393313454624e-05, '"UBE2K"': 4.024196680151708e-05, '"DCLRE1B"': 4.0256627287630445e-05, '"TNPO2"': 4.0292251451576744e-05, '"TUBD1"': 4.029641346571077e-05, '"BICDL1"': 4.029818628030462e-05, '"CLDN15"': 4.031481175074307e-05, '"BCR"': 4.0318382159021695e-05, '"MT-TE"': 4.0320080021582344e-05, '"CAPN15"': 4.0373386531092e-05, '"RAB3D"': 4.0402621542426695e-05, '"MT-TC"': 4.048007038203678e-05, '"RFWD3"': 4.048148488373457e-05, '"MYEF2"': 4.049514170459076e-05, '"ITPK1"': 4.056931698137434e-05, '"LINC01488"': 4.063152268364425e-05, '"KRT81"': 4.064710568845528e-05, '"PLAA"': 4.065859842755108e-05, '"HSPD1P11"': 4.068600162657957e-05, '"CFAP97"': 4.0732314022139945e-05, '"KCNE4"': 4.073590353844109e-05, '"MRPL38"': 4.073956116508487e-05, '"WDR24"': 4.0776199343662464e-05, '"MAP3K2"': 4.07842211235938e-05, '"NACC2"': 4.081460697010245e-05, '"PDCD6IPP2"': 4.0850846846552054e-05, '"POMK"': 4.087786091348404e-05, '"TPP1"': 4.090091561012115e-05, '"NAA50"': 4.090595974248145e-05, '"TMSB4XP4"': 4.0935463158615485e-05, '"GIPR"': 4.093569671842591e-05, '"SMARCD2"': 4.097490352824714e-05, '"BROX"': 4.0993745194520916e-05, '"RABEP1"': 4.0999013413375816e-05, '"LINC00345"': 4.100481073479565e-05, '"FAM177A1"': 4.1010795389689424e-05, '"CNIH3"': 4.1016996296695624e-05, '"MARK2"': 4.1054852549574845e-05, '"LINC02605"': 4.10565370687119e-05, '"ZWILCH"': 4.1066890654059134e-05, '"PCED1B-AS1"': 4.111375571107388e-05, '"COTL1"': 4.111586040458754e-05, '"PLEKHB2"': 4.111868977304638e-05, '"SLC9A3-AS1"': 4.112431014916358e-05, '"TEX261"': 4.113178804174977e-05, '"SDHAF2"': 4.113396631991062e-05, '"ZBTB42"': 4.11468674758734e-05, '"ATP6V0D1-DT"': 4.117526284101171e-05, '"OR7E13P"': 4.117743174151313e-05, '"STX3"': 4.1181988143172346e-05, '"MYO1F"': 4.119832931344102e-05, '"KRT16"': 4.1222257094683175e-05, '"PAQR3"': 4.1228210879541e-05, '"RPS6KA4"': 4.1269436727888195e-05, '"PROM2"': 4.1275065323146097e-05, '"ABCD4"': 4.128161283242542e-05, '"CABLES1"': 4.131045272272934e-05, '"MAMLD1"': 4.131761769177028e-05, '"GRAMD4P3"': 4.132463097886228e-05, '"MNT"': 4.132636818713747e-05, '"BOK"': 4.133567382179162e-05, '"MIPOL1"': 4.135644785600381e-05, '"GALNT18"': 4.1358300368682034e-05, '"SNHG12"': 4.1358610053350914e-05, '"LDLRAP1"': 4.1360541889195344e-05, '"H2AZ2P1"': 4.1375583966812904e-05, '"CRNDE"': 4.1378432849658e-05, '"TMEM191C"': 4.138491226589154e-05, '"PCBP3"': 4.141914234674223e-05, '"MDM1"': 4.142364025718618e-05, '"TWF2"': 4.1428235717054e-05, '"CMTM3"': 4.143341495913579e-05, '"WNT7B"': 4.1433623438101614e-05, '"PTGES2"': 4.144423253660511e-05, '"SPIN1"': 4.145147339896734e-05, '"MT1F"': 4.1452234474611557e-05, '"EIPR1"': 4.145345306853627e-05, '"ARHGEF26"': 4.146038267925103e-05, '"ZBED5-AS1"': 4.1480528486635275e-05, '"SLMAP"': 4.148095280946618e-05, '"FCHO1"': 4.148676839662161e-05, '"MAILR"': 4.149037636485061e-05, '"LNCARSR"': 4.1498738780204535e-05, '"KRT13"': 4.1542131936216255e-05, '"TTC38"': 4.1552567059410067e-05, '"SYNJ2"': 4.156215501148486e-05, '"ZBTB20"': 4.1572008870387546e-05, '"BCL3"': 4.15738255701231e-05, '"SOX9-AS1"': 4.160746591129926e-05, '"KLC1"': 4.161223022867905e-05, '"MT-TS2"': 4.169221118178108e-05, '"NFATC3"': 4.1698420072318076e-05, '"PSORS1C1"': 4.1722414143575145e-05, '"TTC7A"': 4.172701757027498e-05, '"LINC01426"': 4.1727946768990506e-05, '"CASTOR2"': 4.173050330115919e-05, '"TAOK1"': 4.173273476865265e-05, '"ESS2"': 4.173748665380645e-05, '"DEDD"': 4.176370576160391e-05, '"RIPOR1"': 4.177431197370791e-05, '"SP2"': 4.177638848141565e-05, '"TMEM69"': 4.178559729080704e-05, '"TLE2"': 4.1800686450497634e-05, '"CTSL"': 4.1817486025618734e-05, '"CNOT3"': 4.1818388457474024e-05, '"MT-TA"': 4.1836355180991346e-05, '"DPY19L1"': 4.1859775228075785e-05, '"TNFAIP2"': 4.1864493046168554e-05, '"GAS2L1"': 4.1869386508690953e-05, '"WDR26"': 4.188215309154548e-05, '"PRTG"': 4.188522983986195e-05, '"AMIGO1"': 4.1925899792146474e-05, '"SPSB1"': 4.192844398232104e-05, '"LIN52"': 4.195214937934144e-05, '"USP1"': 4.195516633916748e-05, '"DONSON"': 4.196342269579762e-05, '"FBXW5"': 4.1963979591470425e-05, '"ONECUT2"': 4.1967589528696916e-05, '"SIX3"': 4.199896081035294e-05, '"VCAN"': 4.200085014193733e-05, '"MIR3677HG"': 4.203424545491546e-05, '"SLC48A1"': 4.2054939368898064e-05, '"ST6GAL1"': 4.205497456231126e-05, '"CDK6"': 4.225931635216539e-05, '"RAB13"': 4.238560428071055e-05, '"STIMATE"': 4.240963188706826e-05, '"RAB23"': 4.3101541954957846e-05, '"PPP2R5D"': 4.417055339321728e-05, '"PARP9"': 4.417287485867143e-05, '"FNTA"': 4.4682727920275966e-05, '"SECISBP2"': 4.4849368291179506e-05, '"PLCD3"': 4.4940194789933864e-05, '"LRRC59"': 4.50861883625364e-05, '"CAMK2D"': 4.51310685960653e-05, '"MIOS"': 4.544445197767513e-05, '"VMAC"': 4.575157576094303e-05, '"CEP104"': 4.596234927495134e-05, '"CMBL"': 4.673067421989999e-05, '"DDX25"': 4.701354991174263e-05, '"CCNB3P1"': 4.7126370487472036e-05, '"EIF4E"': 4.72205371698331e-05, '"SPAG9"': 4.761743945561284e-05, '"ARHGEF37"': 4.763013271865275e-05, '"HMGA1"': 4.766894745311485e-05, '"RBM12B-AS1"': 4.802153899298641e-05, '"ZMIZ1"': 4.818738613956899e-05, '"KIF16B"': 4.821450306603317e-05, '"TACC2"': 4.824352741413916e-05, '"AFAP1"': 4.885970266243826e-05, '"FAM111B"': 4.9428904090020305e-05, '"LARP1B"': 5.029022182241114e-05, '"SRGAP1"': 5.062065224453059e-05, '"ERBIN"': 5.0779633003247715e-05, '"HYAL2"': 5.092899857087187e-05, '"ITGB8"': 5.106094203904864e-05, '"LINC00491"': 5.1072646521016514e-05, '"FAM13B"': 5.1287669214709796e-05, '"HMGN5"': 5.143080980653732e-05, '"TUBE1"': 5.1598833848779267e-05, '"DCAF6"': 5.168592107784057e-05, '"NAP1L6P"': 5.20503959267163e-05, '"GOLT1A"': 5.2137377113476906e-05, '"NSMCE4A"': 5.214766017441173e-05, '"SLC25A44"': 5.2158979365274606e-05, '"HELB"': 5.2230387767448894e-05, '"ARPP19"': 5.226650338478169e-05, '"PPP4R3A"': 5.227215509797377e-05, '"PRXL2C"': 5.252964197649555e-05, '"SNORC"': 5.255850167995959e-05, '"PRKCD"': 5.2707237022709154e-05, '"KIF1C"': 5.295831878105111e-05, '"TSHZ1"': 5.3164506719921815e-05, '"NRBP1"': 5.323491028380259e-05, '"ASB13"': 5.3868917077142796e-05, '"CEP78"': 5.45971052721929e-05, '"SRM"': 5.462527093694628e-05, '"ROCK1"': 5.4747951039932336e-05, '"CDC25B"': 5.495175042627629e-05, '"FGD5-AS1"': 5.50591715371042e-05, '"PKP1"': 5.5149275588023834e-05, '"ZNF77"': 5.548136527676154e-05, '"HIF1A"': 5.5521762274971706e-05, '"KPNA4"': 5.556299376344341e-05, '"IMPA1"': 5.566627414835785e-05, '"TAOK3"': 5.567705083380426e-05, '"PPRC1"': 5.572335536166955e-05, '"RBBP6"': 5.603419953846791e-05, '"AGO1"': 5.648862140631726e-05, '"DDX28"': 5.659239411867736e-05, '"NDUFAF8"': 5.6621581534046306e-05, '"TRAK1"': 5.666050278837947e-05, '"MFN2"': 5.676010495653204e-05, '"TMEM184C"': 5.691179720163349e-05, '"SLC25A28"': 5.6947653858856655e-05, '"KIF21A"': 5.7006030577492045e-05, '"IKBKG"': 5.715999379021551e-05, '"UIMC1"': 5.716070558350756e-05, '"SINHCAFP3"': 5.722755165491257e-05, '"MDM2"': 5.7310052625310703e-05, '"CNTRL"': 5.739286935880311e-05, '"MYH14"': 5.761894392914144e-05, '"RPS19BP1"': 5.776577848136669e-05, '"PRRT2"': 5.783581864628466e-05, '"ZNF688"': 5.797412816372021e-05, '"RHPN1"': 5.808849668824323e-05, '"UBE2E3"': 5.8110050037591134e-05, '"CDHR3"': 5.8271605844642823e-05, '"EPHX2"': 5.831840509246034e-05, '"LTBR"': 5.840464508382373e-05, '"MASTL"': 5.845018525840056e-05, '"EPN1"': 5.8528136561400486e-05, '"NPM1P40"': 5.853520294812154e-05, '"ZNF2"': 5.8691297463046604e-05, '"TNIP2"': 5.872496598840443e-05, '"LETM1"': 5.876038367190777e-05, '"CES2"': 5.877287799013771e-05, '"WT1-AS"': 5.887398824165827e-05, '"ZC3H10"': 5.8941884494597454e-05, '"ALKBH5"': 5.904197278630901e-05, '"TMEM62"': 5.9044728141628134e-05, '"UBXN2B"': 5.946241723604375e-05, '"CENPU"': 5.9507346487103614e-05, '"ELAC1"': 5.957865001937409e-05, '"KIF18B"': 5.964611043605201e-05, '"RIC1"': 5.9687063837224426e-05, 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'"OR2AT4"': 6.17095784327838e-05, '"TGFB2"': 6.173186848311165e-05, '"SKIDA1"': 6.173382061933026e-05, '"ZNF512B"': 6.179945978630752e-05, '"BOLA3"': 6.181467181508393e-05, '"ZNF85"': 6.184008320152391e-05, '"SEPTIN8"': 6.185878907830524e-05, '"PC"': 6.187110221518516e-05, '"SLK"': 6.188931779162768e-05, '"RASSF3"': 6.199890550032824e-05, '"CKMT1A"': 6.204579958699674e-05, '"MTRNR2L4"': 6.20966913866436e-05, '"SLC4A1"': 6.21183247233267e-05, '"ZZZ3"': 6.212519207011333e-05, '"HAUS1"': 6.213553739800927e-05, '"LIN54"': 6.223015826795796e-05, '"CIAO3"': 6.22335756083433e-05, '"ZNF335"': 6.232672125685314e-05, '"NACC1"': 6.234665715887303e-05, '"ZNF574"': 6.237093436069876e-05, '"SVIL-AS1"': 6.238430328469864e-05, '"SPATA20"': 6.244928289348937e-05, '"LCA5L"': 6.251385431515782e-05, '"MPHOSPH9"': 6.253388896672816e-05, '"PCDHGA10"': 6.259187728150987e-05, '"CEP128"': 6.269940652935993e-05, '"ANKRD13D"': 6.270151310397094e-05, '"LINC02822"': 6.27250032326327e-05, '"DPH1"': 6.276950657111282e-05, '"OR2C3"': 6.283634327608711e-05, '"KPNB1P1"': 6.299998685124945e-05, '"TTYH1"': 6.302729724165778e-05, '"NMI"': 6.312310558762495e-05, '"SAMD8"': 6.321922574508851e-05, '"TBC1D22B"': 6.338084635703668e-05, '"KMT5B"': 6.362338495280632e-05, '"ILRUN"': 6.448530961929815e-05, '"SLC25A37"': 6.450216579859549e-05, '"KCNJ3"': 6.468577956808307e-05, '"LIMK1"': 6.487554424845965e-05, '"PTGES3L"': 6.517100129914404e-05, '"SMG7"': 6.517323411246418e-05, '"ZFC3H1"': 6.544112755772548e-05, '"NAA10"': 6.546114588375473e-05, '"S100A9"': 6.563845557193025e-05, '"OR2I1P"': 6.567254904712095e-05, '"WDFY3"': 6.574610727285282e-05, '"SAP130"': 6.583176513119956e-05, '"RNF130"': 6.597610179864465e-05, '"U2AF1L4"': 6.600028034921977e-05, '"VAX2"': 6.6044260264068e-05, '"CTNNA1-AS1"': 6.63152706010363e-05, '"NCDN"': 6.635026263160749e-05, '"SLC25A24"': 6.692770150079249e-05, '"INPP5A"': 6.696793869254485e-05, '"TCL6"': 6.7024231261967e-05, '"ZFP36L1"': 6.799397284971909e-05, '"PPIG"': 6.807250117179044e-05, '"MAFA"': 6.82043769712283e-05, '"PECR"': 6.822121253078497e-05, '"PDE8A"': 6.846963749007829e-05, '"NDUFS6"': 6.918412549966338e-05, '"ADAMTS19"': 6.921283022780747e-05, '"GNL3L"': 6.923234458246889e-05, '"MAN1A2"': 6.953242737370256e-05, '"LINC00885"': 6.956414338285323e-05, '"MRPL33"': 6.976511668077902e-05, '"QRSL1"': 6.988425510689017e-05, '"GTF3A"': 6.991377003553793e-05, '"CTHRC1"': 6.998607286843767e-05, '"MARCHF6"': 7.063954711048261e-05, '"GHDC"': 7.102475825926716e-05, '"EIF2B4"': 7.140582117232049e-05, '"LXN"': 7.152833007385177e-05, '"INO80E"': 7.161580141275506e-05, '"FRMD3"': 7.186655522490446e-05, '"GALNT1"': 7.197797085569973e-05, '"SRSF1"': 7.198489784183168e-05, '"C8orf88"': 7.207271853268296e-05, '"SLTM"': 7.248148381446236e-05, '"FBXW2"': 7.254426185085361e-05, '"HNRNPD"': 7.273226921055944e-05, '"DHTKD1"': 7.281513440321467e-05, '"ATXN7L1"': 7.294822470358506e-05, '"ARHGAP21"': 7.310685454249093e-05, '"DHX16"': 7.32464990686437e-05, '"RSRC2"': 7.352729035962747e-05, '"ODF2L"': 7.422873818113622e-05, '"RGP1"': 7.423869977473672e-05, '"LYPD4"': 7.428063306387437e-05, '"AURKA"': 7.455701147759563e-05, '"TCHP"': 7.506901175127996e-05, '"LRIF1"': 7.523387042578846e-05, '"TLK2"': 7.544289576776854e-05, '"DPF1"': 7.546498998901216e-05, '"STARD7"': 7.55249413421444e-05, '"NOMO3"': 7.578584083014445e-05, '"KRT10"': 7.597865814289902e-05, '"NIN"': 7.642589345280774e-05, '"NCKAP1"': 7.642855242145654e-05, '"TRIM44"': 7.64676013709883e-05, '"UBE2Q2"': 7.648829230896278e-05, '"NIPSNAP3A"': 7.665600456867681e-05, '"SMPD4BP"': 7.693154529604996e-05, '"ZHX1"': 7.695460308399374e-05, '"PIK3CB"': 7.712490589314193e-05, '"ADD2"': 7.727483476569753e-05, '"AMOTL1"': 7.7296478773675e-05, '"NIBAN2"': 7.738191716013104e-05, '"MAPKAPK2"': 7.760858500740998e-05, '"FAM32A"': 7.765145043887659e-05, '"PLA2G12A"': 7.767993320360651e-05, '"FARP2"': 7.781724184880798e-05, '"MOB3A"': 7.79733557558803e-05, '"SSX2IP"': 7.805491302271281e-05, '"ZNF257"': 7.81510965153435e-05, '"EIF4EBP2"': 7.818608770702665e-05, '"DBF4"': 7.829758052253427e-05, '"MAP3K9"': 7.834519201449633e-05, '"REM2"': 7.847104964755297e-05, '"YARS1"': 7.868224202685655e-05, '"EIF3J"': 7.886586310011838e-05, '"CEBPB"': 7.895825209527754e-05, '"DTX3L"': 7.90396091618937e-05, '"SEC14L2"': 7.918443174961075e-05, '"GRK6"': 7.918961506006094e-05, '"CTBP2"': 7.922915349345628e-05, '"SOX11"': 7.937936009297196e-05, '"OTUD7B"': 7.941452509821779e-05, '"IPPK"': 7.949030945943591e-05, '"ZNF112"': 7.960099548826497e-05, '"USP7"': 7.968186625959201e-05, '"C12orf76"': 8.007264186297624e-05, '"SLC25A23"': 8.009798687046344e-05, '"SETD3"': 8.014518807480744e-05, '"AZI2"': 8.014967916945824e-05, '"CACNA1H"': 8.018442690436661e-05, '"PI4KB"': 8.026287527667007e-05, '"KIF13A"': 8.032352122514247e-05, '"TRAPPC14"': 8.042228261277775e-05, '"MIR99AHG"': 8.054699782136489e-05, '"GADD45GIP1"': 8.058827782999723e-05, '"UBE2J1"': 8.090342656248551e-05, '"RYR3"': 8.096211650896681e-05, '"CCDC186"': 8.098028946620726e-05, '"RAB5C"': 8.103954109388259e-05, '"SLC47A1"': 8.117454656692065e-05, '"MGAT4A"': 8.1266275362643e-05, '"MID2"': 8.135033858233936e-05, '"LRRC37A3"': 8.136188872365783e-05, '"CEP131"': 8.137510709185944e-05, '"PHF21A"': 8.152240428326437e-05, '"ARID1B"': 8.172466486241647e-05, '"EFCAB14"': 8.177307744787985e-05, '"SLC35C2"': 8.196049376793647e-05, '"LACTB2-AS1"': 8.199659035823088e-05, '"BLOC1S3"': 8.208834970422018e-05, '"TOP1MT"': 8.212200157698518e-05, '"EP400P1"': 8.218445468120242e-05, '"STUB1"': 8.220033115168072e-05, '"TRIM3"': 8.228801824495163e-05, '"HIP1"': 8.22921361879877e-05, '"CBX4"': 8.230078454688803e-05, '"SUMO3"': 8.238667642472182e-05, '"SNX25"': 8.240322833530587e-05, '"NR1H2"': 8.258467918099986e-05, '"RRN3P1"': 8.274980245066899e-05, '"TPM1"': 8.296606208516193e-05, '"CORO2A"': 8.296876356099326e-05, '"YAF2"': 8.306991122682155e-05, '"MT-TN"': 8.315498025060685e-05, '"PREB"': 8.343087876459568e-05, '"MBNL3"': 8.361582638724472e-05, '"MYH9"': 8.382236551657123e-05, '"PCP4"': 8.383002459118635e-05, '"TFPI2-DT"': 8.404780921234208e-05, '"MAGI3"': 8.422238442323452e-05, '"RAD23B"': 8.42646084015034e-05, '"CDC42SE1"': 8.427706408230701e-05, '"SMC5"': 8.442032152122961e-05, '"RAPGEF5"': 8.462646213933288e-05, '"SEPTIN11"': 8.497179098939327e-05, '"TMPRSS4"': 8.506231070445773e-05, '"ITPRID2"': 8.529926648447964e-05, '"PCGF3"': 8.5764844012459e-05, '"FAM83H"': 8.579024106259361e-05, '"ADGRV1"': 8.626184020543786e-05, '"CA2"': 8.669996718236906e-05, '"RAB1B"': 8.670233489350588e-05, '"PROSER1"': 8.741955464861619e-05, '"MAFG"': 8.766742828390751e-05, '"RNPS1"': 8.784568084819045e-05, '"PER1"': 8.785592128560609e-05, '"RAD21"': 8.875025081723456e-05, '"SIM2"': 8.878792940492558e-05, '"ANKRD52"': 8.930639576691601e-05, '"PARD3"': 8.946439016620324e-05, '"CETN3"': 8.96585368477088e-05, '"TSHZ2"': 9.001068951858652e-05, '"NFKB1"': 9.032452682029743e-05, '"C6orf62"': 9.049991686476077e-05, '"DNAJC21"': 9.050270635847111e-05, '"PGAM5"': 9.053836130580581e-05, '"COPS9"': 9.09712298122568e-05, '"HCG18"': 9.099317237431269e-05, '"CAV1"': 9.188379818934595e-05, '"PATL1"': 9.227914363236036e-05, '"NGRN"': 9.23358315749992e-05, '"MPDZ"': 9.234423476571939e-05, '"PACS1"': 9.235967549967777e-05, '"PPP1R37"': 9.252880433469837e-05, '"GPATCH4"': 9.289756842494244e-05, '"KCTD3"': 9.300577173737384e-05, '"RBAK"': 9.304883346747918e-05, '"CPSF2"': 9.359250846762835e-05, '"DNAJC2"': 9.430509889095422e-05, '"BTBD6"': 9.43338208653755e-05, '"MT-TS1"': 9.479584868547502e-05, '"CDIPT"': 9.518144688944163e-05, '"LRRCC1"': 9.518393630906533e-05, '"DVL3"': 9.524340083539638e-05, '"MGP"': 9.572117950461056e-05, '"DKC1"': 9.597663665907311e-05, '"EIF2AK1"': 9.60655747278969e-05, '"DLX6-AS1"': 9.647571993995368e-05, '"MCRIP2"': 9.64785597134102e-05, '"CAMK2B"': 9.662339631098651e-05, '"PRPF19"': 9.673268564702342e-05, '"NCALD"': 9.678176578796205e-05, '"REV1"': 9.703853959985417e-05, '"NFKBID"': 9.707593952739142e-05, '"LYAR"': 9.717238237093245e-05, '"ETF1"': 9.76607545199728e-05, '"ADM2"': 9.771532806923903e-05, '"ZC3H13"': 9.778971444113655e-05, '"BCAR1"': 9.797570829787166e-05, '"PLXNA1"': 9.804409747876841e-05, '"GABPB2"': 9.836558034661554e-05, '"CLK2"': 9.846947310784223e-05, '"WWP1"': 9.850986566472096e-05, '"DDX21"': 9.86297210421011e-05, '"SPIRE1"': 9.921759136628771e-05, '"SETD1B"': 9.928725567831308e-05, '"RIPK2"': 9.938984152654767e-05, '"NSD2"': 9.94145081371205e-05, '"POLR3E"': 9.943255748875117e-05, '"AP2S1"': 9.949880811103417e-05, '"KPNA1"': 9.96865542867638e-05, '"FRS2"': 9.984208385672964e-05, '"PRMT2"': 0.00010005113460922467, '"SLAIN2"': 0.00010014364547080167, '"RRP1B"': 0.00010026587977386188, '"C4orf48"': 0.00010077637014630758, '"ASAH2B"': 0.00010152202178833303, '"RP9"': 0.00010154489620154955, '"MT-TD"': 0.00010164594409496931, '"SYTL4"': 0.0001020374310096574, '"FBXL18"': 0.00010207301617509185, '"PSMD5"': 0.00010233807586924854, '"PAPOLA"': 0.00010240647689524124, '"ZNF146"': 0.00010322918641536364, '"SOGA1"': 0.00010341639149835414, '"CDC37"': 0.0001036066468500555, '"ETAA1"': 0.00010361667849781364, '"C2CD2L"': 0.00010371317486044298, '"CCDC51"': 0.00010376009526347104, '"ARHGAP11A"': 0.00010398599337443566, '"YES1"': 0.00010408150739053644, '"PABPN1"': 0.00010431420391493988, '"SMIM15"': 0.00010454752289602937, '"TRIP12"': 0.00010480530801090686, '"STARD10"': 0.00010489833892958428, '"ARHGAP1"': 0.00010549057563099448, '"YTHDF1"': 0.00010585406734051894, '"ROCK2"': 0.00010627498161163756, '"NFX1"': 0.00010687120020127263, '"RAB12"': 0.00010743275376137478, '"FUBP3"': 0.0001074402417044965, '"POLR2J"': 0.00010780517932499065, '"SOS1"': 0.00010832504375723457, '"MTND1P23"': 0.00010859879080036091, '"TCF7"': 0.00010880562316220235, '"PSME4"': 0.0001088224889689461, '"ZNF219"': 0.000109812809345363, '"ISCU"': 0.00011019552490856381, '"CASP8AP2"': 0.00011031434764800294, '"PPM1G"': 0.00011049459913341655, '"FAM102A"': 0.00011089788867047482, '"GCLC"': 0.00011132379165884548, '"METRNL"': 0.00011170544639202552, '"BCCIP"': 0.00011171741862667493, '"CENPF"': 0.00011201171735312281, '"PLBD2"': 0.00011217139588780125, '"RAB39B"': 0.00011231704900326813, '"WDR43"': 0.00011235049639613236, '"HTATSF1"': 0.00011235838731254191, '"RBM23"': 0.00011261399017171288, '"C20orf27"': 0.00011289023695060856, '"BAZ2A"': 0.00011306057383422523, '"ARHGAP5"': 0.00011307395411098766, '"ZNF703"': 0.00011391981334469736, '"PUS7"': 0.00011419175849833968, '"PABPC4"': 0.00011465157651832926, '"TMEM63C"': 0.00011467675082554976, '"CDC42BPB"': 0.00011490201678819606, '"ANKRD11"': 0.00011510648236847668, '"RBBP8"': 0.00011521149018077003, '"SMIM27"': 0.00011634613793954073, '"ZBTB10"': 0.00011651709423718943, '"BTBD9"': 0.00011664654803866613, '"BAZ1B"': 0.00011697306538005129, '"LINC02609"': 0.00011950200025443125, '"H1-2"': 0.00011951890005281567, '"FZD1"': 0.00011960639226999541, '"TWNK"': 0.00011996605676057783, '"ATRX"': 0.00012033221140065063, '"SCYL2"': 0.00012081642734540441, '"NBN"': 0.00012115478625729516, '"KCNC3"': 0.00012139589696638134, '"ZBTB7A"': 0.0001214092712094005, '"MARK3"': 0.0001216535309529742, '"UBALD1"': 0.00012168744164117445, '"CALML5"': 0.00012171708752429533, '"PACS2"': 0.00012173277615854301, '"REV3L"': 0.00012177599490359738, '"DGKZ"': 0.0001218593392702712, '"METRN"': 0.00012186221648211889, '"SMIM10L1"': 0.00012186795537431444, '"NONO"': 0.00012237819762943018, '"CHN1"': 0.00012285611371225645, '"TSPYL1"': 0.0001230484915822453, '"UBE2F"': 0.0001236525811313723, '"KLRG2"': 0.00012412601438572363, '"ZNF48"': 0.000124266104988227, '"NIPBL"': 0.00012432951803727587, '"CCNE1"': 0.00012466097882288154, '"NORAD"': 0.00012479782882813105, '"DNAJA4"': 0.00012511416461536394, '"MYO5C"': 0.0001263985475144565, '"OAZ3"': 0.00012663991119639606, '"MTCH1"': 0.00012709019786318968, '"HPS1"': 0.000127885722333073, '"S100P"': 0.00012845933555462777, '"IRGQ"': 0.00012899076919817696, '"FAM214A"': 0.00012941241382806337, '"CCNI"': 0.00013083823957474485, '"INPP4B"': 0.0001310575247263372, '"PHF20L1"': 0.00013122738313679736, '"GDF15"': 0.00013180173868589473, '"HNRNPH3"': 0.00013202141792152382, '"ARFGEF1"': 0.00013229936744215055, '"PKP3"': 0.00013255933924750176, '"MAGEF1"': 0.00013323258899900514, '"ZBTB37"': 0.0001333881767775585, '"ATF5"': 0.00013442246431172143, '"TBCA"': 0.0001347809382267299, '"MIS12"': 0.00013556200005947376, '"GUCD1"': 0.00013611063843656818, '"NET1"': 0.00013689621908047158, '"UQCC2"': 0.00013832675593241828, '"ARF3"': 0.0001384990225906647, '"ATN1"': 0.00013891987448195486, '"POLR2I"': 0.00013897914200694178, '"PHACTR2"': 0.0001399006757291054, '"SUDS3"': 0.00014008498106501084, '"AAMP"': 0.00014032998351182232, '"NEB"': 0.0001404995080547238, '"SGO1"': 0.00014053962311675152, '"VAV2"': 0.00014056360803753516, '"CAMSAP2"': 0.00014101040009929287, '"ZC3H18"': 0.00014123504211593956, '"SPRYD3"': 0.00014156232187363752, '"LAT2"': 0.0001417665192271411, '"CNBP"': 0.00014219648484407285, '"WASH3P"': 0.00014264336388033845, '"RHOD"': 0.000142768857069748, '"PRR34-AS1"': 0.00014281045914166438, '"ABHD16A"': 0.00014294860153386523, '"SEMA4C"': 0.0001429726269884235, '"LRCH3"': 0.0001430885287082032, '"SMOX"': 0.0001434092368362807, '"POLE"': 0.0001435257794317953, '"PLEKHN1"': 0.00014487647905136365, '"UGDH"': 0.00014549865964405879, '"TASOR2"': 0.0001456315139732506, '"RB1CC1"': 0.000147104908218223, '"PLA2G15"': 0.00014728692615475743, '"EIF1AD"': 0.00014809129484646334, '"FKBP5"': 0.0001482442660550128, '"EPB41L1"': 0.0001489894806199391, '"BOD1L1"': 0.00014934257508358005, '"BTN3A2"': 0.00014959565130910532, '"EGR1"': 0.00014979934813940247, '"TOP2A"': 0.00014983681978706043, '"ZNF347"': 0.0001501235357919199, '"EIF3A"': 0.00015091913953529812, '"TASOR"': 0.0001511887298966543, '"IRX2"': 0.0001523012026191761, '"PRKACA"': 0.00015249326334320756, '"SRP14-DT"': 0.0001530242036126214, '"AREG"': 0.00015330959616750503, '"SYNE2"': 0.0001536285820420611, '"ZNF302"': 0.00015538353007527362, '"TMEM218"': 0.00015634021968518035, '"AP3D1"': 0.00015650093666725538, '"ZMYND11"': 0.00015650563938276625, '"NAA15"': 0.00015716432611477662, '"NEMP1"': 0.00015764827997753812, '"POLDIP2"': 0.00015776517021147838, '"ARHGEF2"': 0.00015818777913266196, '"DNMT1"': 0.00015819407005613937, '"FAM47E"': 0.00015867799901505671, '"MAP7"': 0.00015969635310212268, '"CNOT2"': 0.00016069278746845225, '"HCFC1"': 0.0001612146683470319, '"NOTCH2NLC"': 0.00016134094656115386, '"UHRF1BP1"': 0.00016293480634523675, '"ZNF767P"': 0.00016314628505112078, '"BRIP1"': 0.0001631607189419457, '"PSMD14"': 0.00016338421696269803, '"NMT1"': 0.00016409747805523056, '"NSD1"': 0.00016439800633489925, '"RNF4"': 0.00016537762422938094, '"HBEGF"': 0.00016648755105685018, '"NEDD4L"': 0.0001667046175599675, '"PLEKHF2"': 0.00016693096734180627, '"SESN2"': 0.00016712110349398305, '"MED13"': 0.00016801694393030395, '"ABCB9"': 0.0001680768768057659, '"LEO1"': 0.00016854576136758392, '"BMS1"': 0.0001686892861385436, '"G6PD"': 0.00016869602832325577, '"ATP6V1E1"': 0.0001687326231389183, '"METAP2"': 0.0001696359075665409, '"EIF2AK2"': 0.00017016149598970474, '"ATXN1L"': 0.00017137730297916813, '"C9orf78"': 0.00017178936597413472, '"SUPT6H"': 0.00017180672748813152, '"RPS27L"': 0.0001720235894927778, '"C14orf28"': 0.00017215811680132038, '"USP32"': 0.00017221628280087697, '"KIAA0895L"': 0.00017225508532757057, '"RCC2"': 0.00017391789618867706, '"UBE2Q1"': 0.00017438751233874347, '"MDM4"': 0.0001744730688856348, '"PREX1"': 0.00017497612280886174, '"GASK1B-AS1"': 0.00017665659624727708, '"MLYCD"': 0.000176748029348597, '"MYBL1"': 0.00017712122747618936, '"SLC9A3R1"': 0.00017835929609207277, '"FARSA"': 0.000181633433313012, '"PHF3"': 0.00018165277220933177, '"AFG3L1P"': 0.00018173633326742475, '"LARP1"': 0.00018179542275322924, '"ILF3"': 0.0001824550786119753, '"SSRP1"': 0.00018429836309303345, '"CLIP1"': 0.00018497345222558297, '"ZFAND2A"': 0.0001850788753196073, '"MYO10"': 0.00018549375994077674, '"ZHX3"': 0.00018555870318430595, '"ZNF316"': 0.00018604237249900867, '"CACNA1A"': 0.00018617860716819957, '"GTF2F1"': 0.0001866016761085387, '"PMS2CL"': 0.0001872077683779951, '"MCL1"': 0.00018890179808715572, '"H1-0"': 0.0001903268456320905, '"NOSTRIN"': 0.00019118464771959598, '"PTP4A2"': 0.0001920839832852421, '"ZIC2"': 0.00019287260479161226, '"ZNF165"': 0.00019503186716691623, '"ZFP36"': 0.0001952051831051503, '"NRIP1"': 0.00019691143296407247, '"IWS1"': 0.00019697699715996036, '"NSRP1"': 0.000197821210350498, '"SPRY1"': 0.0001983443773905493, '"TPX2"': 0.00019900630995932096, '"MT-TQ"': 0.0002031590543622397, '"RAD54L"': 0.00020388329241842178, '"GARS1"': 0.0002044155085691336, '"BAP1"': 0.00020481914667920605, '"C8orf33"': 0.00020679167835001985, '"RHOBTB3"': 0.0002068307653087453, '"ZNF580"': 0.00020708136040822862, '"H19"': 0.0002096773859438514, '"MIR663AHG"': 0.00021214570016772023, '"PRRG3"': 0.00021327257092929852, '"PTPN11"': 0.00021379554835459838, '"SYTL2"': 0.0002146514000308209, '"KCNQ1OT1"': 0.00021804145064809112, '"LARP4B"': 0.00021955463869359268, '"CDK2AP1"': 0.00022026292307251514, '"SVIP"': 0.00022062267819958833, '"AATF"': 0.00022126357618296782, '"KPNA2"': 0.00022132684387586018, '"DDX54"': 0.00022145773702423991, '"PRPF40A"': 0.0002215584452563946, '"GDAP2"': 0.00022254945887919715, '"CDKN3"': 0.00022343017104434012, '"PAK2"': 0.00022506872353198726, '"YWHAZ"': 0.0002259700416510612, '"DEK"': 0.00022636069314335738, '"CHMP4B"': 0.00022642525401003101, '"PKP4"': 0.00022905986642862924, '"PMEPA1"': 0.00023107437573306104, '"FBP1"': 0.00023238571227253573, '"IGFBP5"': 0.00023322811912098303, '"CEP55"': 0.000234448414208099, '"NINJ1"': 0.0002351240407495706, '"HNRNPAB"': 0.00023516699919386594, '"STRBP"': 0.000235636020172236, '"H2AC12"': 0.00023566473790260307, '"C7orf50"': 0.00023790633863817717, '"ATP1A1"': 0.00023876334493562088, '"GSPT1"': 0.0002397332684808135, '"MRPS34"': 0.00024143030589071716, '"VPS4A"': 0.00024200016387393807, '"EIF5B"': 0.000244822359238191, '"FGF23"': 0.00024581608874889587, '"ANP32E"': 0.0002489807594711391, '"HAND2-AS1"': 0.00024980531306380163, '"TIMM8B"': 0.00025062201889645606, '"KIF5B"': 0.00025188761423593003, '"DNMT3A"': 0.0002519317170803911, '"XBP1"': 0.0002523973243939284, '"HMGB2"': 0.00025354623486413227, '"RTF1"': 0.0002573111670777858, '"HSPH1"': 0.00025764469712436953, '"BASP1"': 0.00025956396250905443, '"SPDL1"': 0.00025968729704659076, '"H1-3"': 0.00026089307192039563, '"GATA3"': 0.0002631425388969223, '"ATAD2"': 0.00026786444540006485, '"INTS3"': 0.0002685043401226901, '"ENAH"': 0.0002691547609273413, '"NCOR2"': 0.0002691811570273063, '"TPM3"': 0.000269721542064646, '"SMC4"': 0.0002707105906987458, '"HSPD1"': 0.0002713529452473577, '"SPATS2L"': 0.0002729768018776204, '"TARS1"': 0.0002799115262407212, '"WSB2"': 0.00028133775429150897, '"H2AC11"': 0.00028340813269391285, '"H2BC4"': 0.00028725248970738976, '"EBAG9"': 0.00029022425970124305, '"ZC3H15"': 0.00029199344677337686, '"PDAP1"': 0.00029634731726589696, '"ANKIB1"': 0.0002970010287915743, '"RBM25"': 0.0002970301402400427, '"CDV3"': 0.00029938516317198514, '"NCOA3"': 0.0002994401207047055, '"JAK1"': 0.0003012974811918042, '"R3HDM1"': 0.0003085568903792137, '"HDGF"': 0.0003093864253314057, '"RPL37"': 0.0003158559531213767, '"YWHAB"': 0.00031596585369802143, '"CKS2"': 0.00032180313966078544, '"MT2A"': 0.0003272209675293793, '"CBX3"': 0.0003328748989399364, '"GOLGA4"': 0.0003351931829464771, '"TPM4"': 0.0003429138768467658, '"CSDE1"': 0.0003565286009951728, '"NEDD8"': 0.0003602580273947408, '"ZNF217"': 0.00036671429732566813, '"RPL28"': 0.0003671475391749197, '"DNAJA1"': 0.0003696690369188868, '"CAST"': 0.0003771400329378565, '"C2CD2"': 0.0003790278172963413, '"PABPC1"': 0.0003805776424325268, '"EIF4G2"': 0.00039853882978460787, '"HNRNPU"': 0.0003999522400173901, '"HNRNPUL1"': 0.0004027346153410169, '"H1-5"': 0.00040350201989146833, '"PLEC"': 0.00041177456584027086, '"S100A11"': 0.0004220353292370429, '"RPL29"': 0.0004293957940939237, '"H1-4"': 0.00043013318949180465, '"MT-ATP8"': 0.0004393755579204549, '"DSCAM-AS1"': 0.000446377037357132, '"NDUFB2"': 0.0004554004092272626, '"MT-CO1"': 0.00047181723701306675, '"GPM6A"': 0.00047217567626078486, '"FTL"': 0.0004734340755928249, '"CAPZA1"': 0.0004753058349470899, '"NCL"': 0.00047760177658510197, '"CALM2"': 0.0005021741008326336, '"ANP32B"': 0.0005148148222521961, '"RPS6KB1"': 0.0005248771243887997, '"HNRNPA2B1"': 0.0005292131201116971, '"ATP5ME"': 0.000539377346114509, '"PRRC2C"': 0.0005487681738150474, '"PSMA7"': 0.0005504761480183636, '"RPS28"': 0.0005543900968353746, '"TFF3"': 0.0005551987881785038, '"MT-ND1"': 0.0005604975108518916, '"BCAS3"': 0.0005661873718244614, '"RPL11"': 0.0005665868614178883, '"MT-ND6"': 0.0005769621119021687, '"MKI67"': 0.0005869357820648314, '"TPD52L1"': 0.000594942106383743, '"MT-ND4L"': 0.000608569926716786, '"TRIM37"': 0.0006119135256725317, '"MGRN1"': 0.0006119447468571766, '"PFDN4"': 0.0006307913776681197, '"COX7C"': 0.0006324780072910619, '"BPTF"': 0.0006405884007040398, '"KRT8"': 0.000703914673027765, '"RPL37A"': 0.0007074142836545256, '"ELOB"': 0.0007515379859932965, '"ATP5MK"': 0.0007842025861678688, '"MT-ND5"': 0.0007845747432649869, '"HSPB1"': 0.0007999117853388814, '"SERF2"': 0.0008214154520220867, '"RPL23"': 0.0008781821476895891, '"COX7A2"': 0.0008858759488223066, '"UBA52"': 0.0009091878826065128, '"PKIB"': 0.0009727192549003744, '"SET"': 0.0009867480686991746, '"RPS16"': 0.0009923818222538421, '"RPL35A"': 0.0010620356471658329, '"MT-CO2"': 0.0010985656307955997, '"RPS15"': 0.0010988834075067852, '"MT-ND2"': 0.0011460613569253795, '"TOB1"': 0.0012111390880236927, '"VMP1"': 0.0012189299376378858, '"UQCRQ"': 0.001221864922154048, '"RPS27"': 0.0012688288283579173, '"RPL36"': 0.0012940893193163672, '"NEAT1"': 0.0013037871955105342, '"TMEM258"': 0.0013233936328404447, '"SOX4"': 0.0013332769460236748, '"SNRPD2"': 0.001342257975224724, '"ACTB"': 0.00135905465135564, '"PARD6B"': 0.0014236116912495138, '"TMEM64"': 0.0014243012821006321, '"H2AC20"': 0.001569621300904654, '"ROMO1"': 0.0015726059502340526, '"RPS12"': 0.0015959186948774392, '"KRT18"': 0.0017285928000710772, '"RPS15A"': 0.001779134718985919, '"DSP"': 0.0018362698293142253, '"RPLP2"': 0.0018795518343113589, '"RPLP1"': 0.0020557564452875067, '"MT-ATP6"': 0.002093686746590384, '"HES1"': 0.0021227411425202743, '"S100A10"': 0.002186966306547731, '"RPL34"': 0.0022159112080691002, '"RPL39"': 0.002488307578889406, '"RPL30"': 0.0026747534742965966, '"RPL15"': 0.0032566606507516676, '"RPL12"': 0.0034849543641418206, '"MT-CYB"': 0.0035222760495261757, '"RPS5"': 0.0038543351696016023, '"H4C3"': 0.004032532029166162, '"BCYRN1"': 0.004070369924364481, '"MT-ND3"': 0.004333515549134206, '"MT-ND4"': 0.004536968455553641, '"TPI1"': 0.005034188148293925, '"MALAT1"': 0.006410534985500221, '"MT-CO3"': 0.006913490199395791, '"PKM"': 0.007644018041961665, '"RPL35"': 0.008295266582972713, '"RPL13"': 0.012629847220402805, '"ENO1"': 0.013250379557480704, '"RPS14"': 0.014401267144233376, '"RPS19"': 0.019089578605601325, '"MT-RNR1"': 0.021540918223268778, '"LGALS1"': 0.02419628358724785, '"KRT19"': 0.04548687024222743, '"TMSB10"': 0.05581814376350895, '"PGK1"': 0.06250162044436891, '"GAPDH"': 0.08547181749177711, '"MT-RNR2"': 0.11641265860620124, '"TFF1"': 0.28485557430418823}

To see the differences in distribution of the gene, we plot some boxplots.

In [ ]:
Gene_Hypo = MCF7_drop_Hypo_f_n_trans['"TFF1"']
Gene_Hypo
Out[ ]:
"AAAAAATCCGGC_Hypoxia"    9
"AAAAACACGATC_Hypoxia"    1
"AAAAATGGGGGA_Hypoxia"    1
"AAAACATCTTGC_Hypoxia"    1
"AAAACCAGCCCA_Hypoxia"    4
                         ..
"TTTTCGCGTAGA_Hypoxia"    3
"TTTTCGTCCGCT_Hypoxia"    4
"TTTTCTCCGGCT_Hypoxia"    2
"TTTTGTTCAAAG_Hypoxia"    6
"TTTTTTGTATGT_Hypoxia"    0
Name: "TFF1", Length: 8921, dtype: int64
In [ ]:
Gene_Norm = MCF7_drop_Norm_f_n_trans['"TFF1"']
Gene_Norm
Out[ ]:
"AAAAACCTATCG_Normoxia"    4
"AAAACAACCCTA_Normoxia"    1
"AAAACACTCTCA_Normoxia"    1
"AAAACCAGGCAC_Normoxia"    1
"AAAACCTAGCTC_Normoxia"    0
                          ..
"TTTTTACCTCCC_Normoxia"    0
"TTTTTCGAATCA_Normoxia"    2
"TTTTTCGACCAC_Normoxia"    4
"TTTTTGCGCCAT_Normoxia"    4
"TTTTTTGTCATA_Normoxia"    1
Name: "TFF1", Length: 12705, dtype: int64
In [ ]:
Gene_Hypo.describe()
Out[ ]:
count    8921.000000
mean        3.293241
std         3.071657
min         0.000000
25%         1.000000
50%         3.000000
75%         5.000000
max        46.000000
Name: "TFF1", dtype: float64
In [ ]:
Gene_Norm.describe()
Out[ ]:
count    12705.000000
mean         0.750413
std          1.108189
min          0.000000
25%          0.000000
50%          0.000000
75%          1.000000
max          9.000000
Name: "TFF1", dtype: float64
In [ ]:
plt.figure(figsize=(16,16))
sns.boxplot(data=[Gene_Norm, Gene_Hypo])
plt.xticks(ticks = [0, 1], labels=["Normoxic", "Hypoxic"])
plt.title("TFF1")
plt.show()

We can see from the plot that the gene TFF1 has very different distribution between the hypoxic and the normoxic cells. What we can definetely see is that the outliners are very different.

Clustering Data

To better visualize the data, we performed a PCA in 2 dimensions and then used the data for K-means clustering. In such a way, we are trying to split the data in two groups and, by using different colours for hypoxic and normoxic cells, check whether the clustering assigned them correctly.

In [ ]:
from sklearn.decomposition import PCA
In [ ]:
from sklearn.cluster import KMeans
In [ ]:
def plot_data_C(X, col):
  for i in range(len(X)):
    plt.plot(X[i][0], X[i][1], 'k.', markersize=2, c=col[i])

def plot_centroids_C(centroids, weights=None, circle_color='w', cross_color='k'):
    if weights is not None:
        centroids = centroids[weights > weights.max() / 10]
    plt.scatter(centroids[:, 0], centroids[:, 1],
                marker='o', s=35, linewidths=8,
                color=circle_color, zorder=10, alpha=0.9)
    plt.scatter(centroids[:, 0], centroids[:, 1],
                marker='x', s=2, linewidths=12,
                color=cross_color, zorder=11, alpha=1)

def plot_decision_boundaries(clusterer, X, col, resolution=1000, show_centroids=True,
                             show_xlabels=True, show_ylabels=True):
    mins = X.min(axis=0) - 0.1
    maxs = X.max(axis=0) + 0.1
    xx, yy = np.meshgrid(np.linspace(mins[0], maxs[0], resolution),
                         np.linspace(mins[1], maxs[1], resolution))
    Z = clusterer.predict(np.c_[xx.ravel(), yy.ravel()])
    Z = Z.reshape(xx.shape)

    plt.contourf(Z, extent=(mins[0], maxs[0], mins[1], maxs[1]),
                cmap="Pastel2")
    plt.contour(Z, extent=(mins[0], maxs[0], mins[1], maxs[1]),
                linewidths=1, colors='k')
    plot_data_C(X, col)
    if show_centroids:
        plot_centroids_C(clusterer.cluster_centers_)

    if show_xlabels:
        plt.xlabel("$x_1$", fontsize=14)
    else:
        plt.tick_params(labelbottom=False)
    if show_ylabels:
        plt.ylabel("$x_2$", fontsize=14, rotation=0)
    else:
        plt.tick_params(labelleft=False)
In [ ]:
pcaM = PCA(n_components = 2)
MCF7_drop_lowT = pcaM.fit_transform(MCF7_drop_f_n.T)
MCF7_drop_ret = pcaM.inverse_transform(MCF7_drop_lowT)
print(MCF7_drop_lowT.shape)
(21626, 2)
In [ ]:
col = []
for c in MCF7_drop_f_n.columns:
  if "Hypo" in c:
    col.append("r")
  else:
    col.append("b")
print(len(col))
21626
In [ ]:
index = MCF7_drop_f_n.T.index
MCF7_drop_hyponormo = np.zeros((len(index)), dtype = 'int64')
for i in range(len(index)):
    MCF7_drop_hyponormo[i] = not 'Hypo' in index[i] # 0 Hypo 1 Norm
In [ ]:
from sklearn import metrics
k = 2
for i in [45, 52, 30, 37, 67]:
  kmeans = KMeans(n_clusters=k, random_state=i)
  y_pred = kmeans.fit_predict(MCF7_drop_lowT)
  mapping = {}
  for class_id in np.unique(MCF7_drop_hyponormo):
      mode, _ = stats.mode(y_pred[MCF7_drop_hyponormo==class_id]) # look at all samples with a given label and study what is the most common label given by the Gaussian mixture
      mapping[mode[0]] = class_id
  #y_pred = np.array([mapping[cluster_id] for cluster_id in y_pred])
  # print(accuracy_score(y_pred, MCF7_hyponormo))
  print("fraction of correct predictions", np.sum(y_pred==MCF7_drop_hyponormo) / len(y_pred))
  plt.figure(figsize=(8, 4))
  plot_decision_boundaries(kmeans, MCF7_drop_lowT, col)
  plt.show()
fraction of correct predictions 0.45440673263664105
fraction of correct predictions 0.45440673263664105
fraction of correct predictions 0.45440673263664105
fraction of correct predictions 0.45440673263664105
fraction of correct predictions 0.4456210117451216

We tried to use different random states to calculate an average score of our K-means clustering. We can see that it predicts correctly only around 44% of the data in every case, this is probably due to the fact that a PCA in 2 dimention retain low variance in this particular dataset.

Let's now try clustering without applying PCA.

In [ ]:
from sklearn import metrics
k = 2
accuracy_scores = []
for i in [42, 48, 28, 37, 67]:
  kmeans = KMeans(n_clusters=k, random_state=i)
  y_pred = kmeans.fit_predict(MCF7_drop_f_n.T)
  mapping = {}
  for class_id in np.unique(MCF7_drop_hyponormo):
      mode, _ = stats.mode(y_pred[MCF7_drop_hyponormo==class_id]) # look at all samples with a given label and study what is the most common label given by the Gaussian mixture
      mapping[mode[0]] = class_id
  # y_pred = np.array([mapping[cluster_id] for cluster_id in y_pred])
  print(accuracy_score(MCF7_drop_hyponormo, y_pred))
  print("fraction of correct predictions", np.sum(y_pred==MCF7_drop_hyponormo) / len(y_pred))
  accuracy_scores.append(accuracy_score(MCF7_drop_hyponormo, y_pred))
0.5456395079996301
fraction of correct predictions 0.5456395079996301
0.5456395079996301
fraction of correct predictions 0.5456395079996301
0.5456395079996301
fraction of correct predictions 0.5456395079996301
0.5456395079996301
fraction of correct predictions 0.5456395079996301
0.5456395079996301
fraction of correct predictions 0.5456395079996301
In [ ]:
print("Average accuracy score:", sum(accuracy_scores)/len(accuracy_scores))
Average accuracy score: 0.5456395079996301

We then repeated the clustering using the dataset not processed by the PCA, obtaining a slightly higher accuracy score. Even using the whole dataset, the clustering accuracy is still pretty low.

In [ ]:
from sklearn.cluster import kmeans_plusplus

k = 2
accuracy_scores = []
for i in [85, 42, 65, 98, 200]:
  centroids, indices = kmeans_plusplus(MCF7_drop_f_n.T.to_numpy(), n_clusters = 2, random_state=i)
  kmeans = KMeans(n_clusters=k, random_state=i)
  kmeans.fit(centroids)
  y_pred = kmeans.predict(MCF7_drop_f_n.T)
  mapping = {}
  for class_id in np.unique(MCF7_drop_hyponormo):
      mode, _ = stats.mode(y_pred[MCF7_drop_hyponormo==class_id]) # look at all samples with a given label and study what is the most common label given by the Gaussian mixture
      mapping[mode[0]] = class_id
  # y_pred = np.array([mapping[cluster_id] for cluster_id in y_pred])
  print(accuracy_score(MCF7_drop_hyponormo, y_pred))
  #print("fraction of correct predictions", np.sum(y_pred==MCF7_hyponormo) / len(y_pred))
  accuracy_scores.append(accuracy_score(MCF7_drop_hyponormo, y_pred))
print("Average accuracy score:", sum(accuracy_scores)/len(accuracy_scores))
0.48552668084712847
0.7900675113289559
0.519374826597614
0.7744381762693054
0.6864422454452973
Average accuracy score: 0.6511698880976602

We finally tried to find the centroids using K-means++ and then used them to cluster the data. We can see that the result is a little better than the previous case where we used K-means.

HCC1806

Understanding the data
In [ ]:
HCC1806_drop_f_n_describe = HCC1806_drop_f_n.describe()
HCC1806_drop_f_n_describe
Out[ ]:
"AAAAAACCCGGC_Normoxia" "AAAACCGGATGC_Normoxia" "AAAACGAGCTAG_Normoxia" "AAAACTTCCCCG_Normoxia" "AAAAGCCTACCC_Normoxia" "AAACACAAATCT_Normoxia" "AAACCAAGCCCA_Normoxia" "AAACCATGCACT_Normoxia" "AAACCTCCGGCT_Normoxia" "AAACGCCGGTCC_Normoxia" ... "TTTTCTGATGGT_Hypoxia" "TTTTGATTCAGA_Hypoxia" "TTTTGCAACTGA_Hypoxia" "TTTTGCCGGGCC_Hypoxia" "TTTTGTTAGCCT_Hypoxia" "TTTTTACCAATC_Hypoxia" "TTTTTCCGTGCA_Hypoxia" "TTTTTGCCTGGG_Hypoxia" "TTTTTGTAACAG_Hypoxia" "TTTTTTTGAATC_Hypoxia"
count 3000.00000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.00000 3000.000000 3000.000000 ... 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000 3000.000000
mean 0.02900 0.041667 0.024333 0.021667 0.029667 0.020000 0.036000 0.02600 0.034000 0.029333 ... 0.043000 0.049667 0.037000 0.047667 0.057000 0.023333 0.041667 0.041667 0.043333 0.040000
std 0.23276 0.309778 0.231860 0.189409 0.323761 0.170126 0.250449 0.23525 0.231362 0.218683 ... 0.271739 0.319219 0.279864 0.259648 0.304053 0.214797 0.236536 0.285116 0.267356 0.282418
min 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
25% 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
50% 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
75% 0.00000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.00000 0.000000 0.000000 ... 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
max 5.00000 9.000000 7.000000 4.000000 12.000000 3.000000 4.000000 6.00000 4.000000 4.000000 ... 4.000000 7.000000 7.000000 4.000000 5.000000 4.000000 4.000000 5.000000 5.000000 6.000000

8 rows × 14682 columns

In [ ]:
sns.displot(data = HCC1806_drop_f_n_describe.iloc[1], bins=50, color="teal")
plt.show()
In [ ]:
sns.displot(data = HCC1806_drop_f_n_describe.iloc[6], bins=50, color="teal")
plt.show()
Hypo vs Norm
In [ ]:
HCC1806_drop_Hypo_f_n = HCC1806_drop_f_n.loc[:, HCC1806_drop_f_n.columns.str.contains('Hypoxia')]
HCC1806_drop_Hypo_f_n
Out[ ]:
"AAAAACGTCACT_Hypoxia" "AAAAAGCACTTG_Hypoxia" "AAAACAGCACAG_Hypoxia" "AAAACCTCGGGT_Hypoxia" "AAAACCTGCGCT_Hypoxia" "AAAACGCCGACA_Hypoxia" "AAAACGTCTCGT_Hypoxia" "AAAACGTTCGGT_Hypoxia" "AAAACTCTTGTT_Hypoxia" "AAAAGAACTCCT_Hypoxia" ... "TTTTCTGATGGT_Hypoxia" "TTTTGATTCAGA_Hypoxia" "TTTTGCAACTGA_Hypoxia" "TTTTGCCGGGCC_Hypoxia" "TTTTGTTAGCCT_Hypoxia" "TTTTTACCAATC_Hypoxia" "TTTTTCCGTGCA_Hypoxia" "TTTTTGCCTGGG_Hypoxia" "TTTTTGTAACAG_Hypoxia" "TTTTTTTGAATC_Hypoxia"
"H1-5" 5 0 0 0 0 0 0 0 0 0 ... 0 1 0 2 1 0 0 0 3 1
"MALAT1" 0 4 0 0 1 2 0 2 0 2 ... 3 1 1 1 4 0 4 1 3 6
"MT-RNR2" 0 0 3 1 0 3 0 0 0 0 ... 1 2 2 2 0 0 1 0 1 0
"ARVCF" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"BCYRN1" 0 0 0 0 0 1 2 0 0 0 ... 1 1 0 1 1 0 0 1 0 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
"SCCPDH" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"NTAN1" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 1 0 0 0 0 0
"CLIP2" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"DUSP23" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"ZNF682" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0

3000 rows × 8899 columns

In [ ]:
HCC1806_drop_Norm_f_n = HCC1806_drop_f_n.loc[:, HCC1806_drop_f_n.columns.str.contains('Normoxia')]
HCC1806_drop_Norm_f_n
Out[ ]:
"AAAAAACCCGGC_Normoxia" "AAAACCGGATGC_Normoxia" "AAAACGAGCTAG_Normoxia" "AAAACTTCCCCG_Normoxia" "AAAAGCCTACCC_Normoxia" "AAACACAAATCT_Normoxia" "AAACCAAGCCCA_Normoxia" "AAACCATGCACT_Normoxia" "AAACCTCCGGCT_Normoxia" "AAACGCCGGTCC_Normoxia" ... "TTTGTATGCGTC_Normoxia" "TTTGTATTTTCG_Normoxia" "TTTGTCCTTGTA_Normoxia" "TTTTACTCGATG_Normoxia" "TTTTAGCTTTCA_Normoxia" "TTTTATACGAGA_Normoxia" "TTTTCTTCCGAC_Normoxia" "TTTTGGCGGTCA_Normoxia" "TTTTGTAAGGGA_Normoxia" "TTTTGTCGGGCA_Normoxia"
"H1-5" 2 2 5 1 0 0 0 0 1 0 ... 0 4 1 3 0 0 0 3 1 3
"MALAT1" 3 3 2 3 12 3 1 2 0 0 ... 3 1 6 2 3 1 4 2 4 5
"MT-RNR2" 0 0 0 0 0 0 0 0 0 1 ... 1 0 1 0 0 0 0 0 1 0
"ARVCF" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"BCYRN1" 0 1 1 0 0 1 1 2 0 3 ... 1 0 0 1 1 0 0 0 0 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
"SCCPDH" 0 0 0 0 0 0 0 0 0 0 ... 0 1 0 0 0 0 0 0 0 0
"NTAN1" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"CLIP2" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"DUSP23" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
"ZNF682" 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0

3000 rows × 5783 columns

In [ ]:
df_small = HCC1806_drop_Norm_f_n.transpose().iloc[0:, :50]
plt.figure(figsize=(16,4))
plot=sns.violinplot(data=df_small,palette="Set3",cut=0)
plt.setp(plot.get_xticklabels(), rotation=90)
plt.show()
In [ ]:
df_small = HCC1806_drop_Hypo_f_n.transpose().iloc[0:, :50]
plt.figure(figsize=(16,4))
plot=sns.violinplot(data=df_small,palette="Set3",cut=0)
plt.setp(plot.get_xticklabels(), rotation=90)
plt.show()

It is quite hard to see a major difference.\ We again compute the ratio of the log_2 of the mean + 1.

In [ ]:
HCC1806_drop_Hypo_f_n_trans = HCC1806_drop_Hypo_f_n.T
HCC1806_drop_Norm_f_n_trans = HCC1806_drop_Norm_f_n.T
In [ ]:
HCC1806_drop_Hypo_f_n_trans_d = HCC1806_drop_Hypo_f_n.T.describe()
HCC1806_drop_Norm_f_n_trans_d = HCC1806_drop_Norm_f_n.T.describe()
In [ ]:
HCC1806_drop_f_n_logratio = np.log2(HCC1806_drop_Hypo_f_n_trans_d.iloc[1] + 1) - np.log2(HCC1806_drop_Norm_f_n_trans_d.iloc[1] + 1)
HCC1806_drop_f_n_logratio.sort_values(ascending=False)
Out[ ]:
"IGFBP3"      0.525908
"FGF23"       0.487667
"LDHA"        0.482526
"NDRG1"       0.444544
"GPM6A"       0.422501
                ...   
"HSP90AB1"   -0.445329
"HSPD1"      -0.471334
"HSP90AA1"   -0.505334
"AKR1C2"     -0.570131
"BCYRN1"     -0.657697
Name: mean, Length: 3000, dtype: float64

Apparently, the gene IGFBP3 is the most important in the HCC1806 dropseq dataset.

Check with random forest which cells have higher importance

We now try to get the most important genes with a random forest to check wheter they are the same as the ones we found before.

In [ ]:
data_test = HCC1806_drop_f_n
In [ ]:
# Let's load the packages
import numpy as np
import pandas as pd
from sklearn.datasets import load_boston
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestRegressor
from sklearn.inspection import permutation_importance
#import shap
from matplotlib import pyplot as plt

plt.rcParams.update({'figure.figsize': (12.0, 8.0)})
plt.rcParams.update({'font.size': 14})
In [ ]:
index = data_test.T.index
y = np.zeros((len(index)),dtype = 'int64')
for i in range(len(index)):
    y[i] = not 'Hypo' in index[i] # 0 Hypo 1 Norm
In [ ]:
X_train, X_test, y_train, y_test = train_test_split(data_test.T, y, test_size= 0.1, random_state= 42)
In [ ]:
rf = RandomForestRegressor(n_estimators=10)
rf.fit(X_train, y_train)
Out[ ]:
RandomForestRegressor(n_estimators=10)
In [ ]:
genes_importance = rf.feature_importances_
In [ ]:
genes = {}
for n, g in zip(data_test.index, genes_importance):
  genes[n] = g
print({k: v for k, v in sorted(genes.items(), key=lambda item: item[1], reverse=True)})
{'"NDRG1"': 0.11017108099979633, '"AKR1C2"': 0.10412354009140996, '"IGFBP3"': 0.06267123259196629, '"FGF23"': 0.05028077890515501, '"WDR43"': 0.03291294712318751, '"BCYRN1"': 0.031017949233915258, '"LDHA"': 0.02923350303600919, '"GPM6A"': 0.02215913052583788, '"HSP90AA1"': 0.01954481606682723, '"RPL41"': 0.018503503041994183, '"HSPD1"': 0.01521398925790309, '"EIF3J"': 0.013421127989964313, '"TMSB10"': 0.011685154891367018, '"AKR1C1"': 0.010570605898465497, '"NCL"': 0.01055285492010248, '"RPS28"': 0.009468107164498876, '"S100A10"': 0.007938665660892828, '"MALAT1"': 0.007638317711998487, '"ENO1"': 0.00753051878369682, '"EGLN3"': 0.006493533999303821, '"BNIP3"': 0.006487001514071113, '"NPM1P40"': 0.006086094091231668, '"KRT19"': 0.006001004129403219, '"HSP90AB1"': 0.00596361843743688, '"RPS27"': 0.005354758165214481, '"PGK1"': 0.00472678521672826, '"H4C3"': 0.004520148554145522, '"HSP90B1"': 0.004467412099537724, '"FTL"': 0.004447793628914251, '"ZC3H15"': 0.004387837743840847, '"MT-RNR2"': 0.004101299582630042, '"B4GALT1"': 0.003933912858548733, '"P4HA1"': 0.003740750944855744, '"MT-TV"': 0.0031023417486446153, '"H2AC12"': 0.002995303612343034, '"RPL35"': 0.0029750802745726933, '"RPLP1"': 0.0027851340383064273, '"PLEC"': 0.0027792545992741413, '"NCALD"': 0.0027009453504468492, '"RPS5"': 0.002678666773893195, '"RPL8"': 0.002664050357012829, '"S100A11"': 0.002591190912301445, '"CALM2"': 0.002469512531253525, '"NEAT1"': 0.0023997483972577976, '"MT-TQ"': 0.002193921280561021, '"PSMA7"': 0.0021931269362724707, '"BNIP3L"': 0.0021710099829992512, '"MARCKS"': 0.0020248640977330408, '"BTBD9"': 0.0020232340575063856, '"SERF2"': 0.0020219946140690717, '"RPLP2"': 0.001919142850090759, '"RPL39"': 0.0018919158511813787, '"YBX1"': 0.0017773290857469228, '"EEF2"': 0.0017650241606356476, '"FOSL1"': 0.001751848288991023, '"CAV1"': 0.001634266889971502, '"MT2A"': 0.0015984518782531313, '"RPL10"': 0.0015934460680263676, '"RPL27A"': 0.001570131229194538, '"SFN"': 0.0015695896986519583, '"PTMS"': 0.0015628796880904309, '"AHNAK2"': 0.0015503437237867808, '"CNNM2"': 0.0015486647949964705, '"CACNA1A"': 0.0015069041533679968, '"H1-3"': 0.0014933048977463694, '"RPS14"': 0.0014894713584294318, '"RPL21"': 0.0014714062727704765, '"RPS15"': 0.001388783900542571, '"GSTP1"': 0.0013413501830673359, '"H2AC11"': 0.0013281911796263423, '"HNRNPU"': 0.0013231478148974817, '"YWHAZ"': 0.0012862580396838948, '"RPL37A"': 0.0012714575125409799, '"POLR2L"': 0.0012628131438675318, '"H1-5"': 0.0012376617979422751, '"RPL28"': 0.0012281776596877246, '"CAST"': 0.001225159919916652, '"EZR"': 0.001225071329272939, '"TPT1"': 0.001205269850064627, '"RPS2"': 0.001194308768976981, '"RPL12"': 0.001191439778123696, '"HEPACAM"': 0.0011808849339063172, '"CALR"': 0.0011766494654636482, '"MIR663AHG"': 0.0011740428840993527, '"S100A6"': 0.0011683803025887224, '"HNRNPA2B1"': 0.0011433367372421274, '"PDIA3"': 0.0011427988989764011, '"RPL35A"': 0.001138043526614551, '"DNMT1"': 0.0011345871990638581, '"GOLGA4"': 0.0011184204515008703, '"LAMB3"': 0.0010941455176156183, '"EEF1A1"': 0.001035502143109066, '"KRT7"': 0.001025111371904589, '"TPI1"': 0.0010037770005445342, '"RPS3"': 0.0009992763649978413, '"RPL13"': 0.0009988530531959234, '"DSP"': 0.0009954796289557675, '"ATAD2"': 0.0009954073197492503, '"UQCR11"': 0.0009797563088148648, '"ATP5F1E"': 0.0009595705909231783, '"H3C2"': 0.0009558964721222386, '"GDPGP1"': 0.0009519222329638932, '"RPS21"': 0.0009443610091810247, '"ANP32B"': 0.0009438497352050117, '"TMSB4X"': 0.0009418706316113773, '"MT-RNR1"': 0.0009358881385485034, '"H1-2"': 0.0009135586157927686, '"ZBTB20"': 0.0009128474780133695, '"MT1X"': 0.0009072928666512218, '"PABPC1"': 0.0009066193557225819, '"BAP1"': 0.0009048023210422446, '"RPS12"': 0.0008949506848809207, '"TPX2"': 0.000890948270108415, '"H4C5"': 0.0008795940130621462, '"STMN1"': 0.0008737086642316875, '"COPS9"': 0.0008598763456278156, '"CCDC34"': 0.0008592509955289553, '"RAC1"': 0.0008575683934681928, '"MYH9"': 0.000855640858443516, '"AHNAK"': 0.0008553711742835025, '"H1-1"': 0.0008539692925172671, '"HNRNPM"': 0.0008502139217454942, '"RPL36"': 0.0008413806930741123, '"HSPB1"': 0.0008378221191292903, '"CAP1"': 0.0008247117773191265, '"FABP5"': 0.0008191045457619936, '"GAPDH"': 0.0008099000546113184, '"RTF1"': 0.000805840949478334, '"HSPA5"': 0.0008030834561066058, '"KIF5B"': 0.0007893887567876539, '"CENPF"': 0.0007864922979953076, '"RPS19"': 0.000783543934948658, '"KCNJ3"': 0.0007817701081982712, '"HMGB2"': 0.0007809003567787343, '"GTF3A"': 0.0007751059948149785, '"NDUFB2"': 0.0007742983985061338, '"LIMCH1"': 0.0007729484995453888, '"MT-ND1"': 0.0007601737159585914, '"NEDD4L"': 0.0007269538533794223, '"RPSA"': 0.0007253343985169863, '"RPL37"': 0.0007200553039830877, '"KDM1A"': 0.0007198692873801266, '"PDIA6"': 0.0007185432281811555, '"ELOB"': 0.000717755412176585, '"YBX3"': 0.0007168112219539225, '"MT-ND2"': 0.0007149357749625225, '"ZNF302"': 0.0007147231528305951, '"SLC25A48"': 0.0007127806117647259, '"ACTG1"': 0.0007080842913453339, '"PFN1"': 0.0007009353815375238, '"RPL18"': 0.0006980952510066309, '"KRT13"': 0.0006911468454522127, '"UQCRQ"': 0.0006763182602536993, '"METTL26"': 0.0006722065897849059, '"PPDPF"': 0.000667262716795998, '"ANXA1"': 0.000665092935494461, '"PDCD4"': 0.0006611275255486596, '"TMEM160"': 0.0006595305306552422, '"H1-4"': 0.000632803829471708, '"C4orf3"': 0.0006304991309298669, '"GBP1P1"': 0.0006131868310168865, '"KRT10"': 0.0006067722931474635, '"MT-ND4L"': 0.0005987771402451838, '"PRMT2"': 0.0005986055143350369, '"TMA7"': 0.0005959467587331245, '"RPS8"': 0.0005929918522310468, '"GPI"': 0.0005927958262165032, '"CBX3"': 0.0005919036418648444, '"MRPL55"': 0.0005847441746237499, '"RBM23"': 0.0005844451475604752, '"SNRNP70"': 0.0005743624195706353, '"TOP2A"': 0.0005718345157763944, '"FGFR1OP2"': 0.0005700015830417413, '"RAB4A"': 0.0005686202364119833, '"HMGA1"': 0.0005681849058004241, '"MT-CO2"': 0.000564378438966458, '"PLBD2"': 0.0005573665474277789, '"GUK1"': 0.0005514852555694694, '"ATOX1"': 0.0005494395131447357, '"RRS1"': 0.0005484191019273374, '"MZT2B"': 0.0005474191500048607, '"FLNA"': 0.0005462958889448675, '"STRN4"': 0.0005456492112037108, '"ZBTB33"': 0.0005349652600099973, '"S100A2"': 0.0005337622122217089, '"TSR1"': 0.0005305574740182297, '"MT-CO3"': 0.0005249976432624325, '"LBH"': 0.0005040528782945797, '"SLC25A53"': 0.0005020867463688065, '"HMGN3"': 0.0004973207434192626, '"RPS6KA6"': 0.0004957658264686902, '"RPL18A"': 0.0004955480378029153, '"SNHG9"': 0.0004945823833645541, '"PRRG3"': 0.0004934679595819938, '"SHOX"': 0.0004917225983215569, '"CAVIN1"': 0.0004882713077240299, '"KIAA1522"': 0.0004867363448646368, '"MKI67"': 0.0004864480080550832, '"FAM120A"': 0.00048459548494541037, '"NDUFB1"': 0.0004810422004718799, '"ZHX1"': 0.00047917768851362004, '"POLR2A"': 0.00047769979941288164, '"C19orf53"': 0.0004758452390637677, '"TMEM141"': 0.0004689799961638787, '"FUBP3"': 0.0004670429393451198, '"MRPL33"': 0.00046557188716919744, '"DDX54"': 0.00046506020400071844, '"PRRC2A"': 0.0004620988233756909, '"YTHDC1"': 0.0004596165412689891, '"FOXP1"': 0.0004583338939235477, '"PKM"': 0.0004582663413994382, '"UTP3"': 0.00045591377925683214, '"HDGF"': 0.0004552017480606947, '"BTN3A2"': 0.00045452858638629184, '"OAZ1"': 0.0004532228008441457, '"APLP2"': 0.00045087891198505013, '"TTC19"': 0.00045061485020778894, '"SPRR1B"': 0.0004418578340316488, '"HCFC1"': 0.00043937438837525386, '"ATP1A1"': 0.00043543306819751636, '"KRT14"': 0.00043530788975727183, '"ATP5ME"': 0.0004334695457147258, '"KIF3B"': 0.00043296428410983384, '"ZNF99"': 0.0004312493749606864, '"SETD2"': 0.00043070678188379273, '"CYB5R3"': 0.00042659849380268834, '"PSMG1"': 0.0004262826913399028, '"EGR1"': 0.0004261863544911959, '"NCOR2"': 0.00042505613039386795, '"TAF15"': 0.00042214590027358953, '"FAM83G"': 0.00042126243504300704, '"FEM1A"': 0.00041913815776270627, '"CFAP251"': 0.00041894988458829406, '"PHGDH"': 0.0004187227348798748, '"DCTN1"': 0.00041842761991512067, '"DEK"': 0.00041697070485950574, '"MT-CO1"': 0.0004123672458284964, '"SAMD4A"': 0.00041162889895152404, '"CAMSAP2"': 0.0004114440410623338, '"ARF3"': 0.00041061515430186157, '"PTGR1"': 0.00040623595999180297, '"DAAM1"': 0.0004058594411617929, '"MLLT10"': 0.0004051208928032575, '"ARID5B"': 0.0004032519808955139, '"KIFC2"': 0.0004026286921292626, '"MZT2A"': 0.0004022934574182509, '"SH3RF1"': 0.0004004303175508885, '"MT-TS2"': 0.00039594299903225665, '"ZNF609"': 0.0003940495589966339, '"MKNK1"': 0.0003909683636813587, '"ZNF316"': 0.0003876676656223401, '"S1PR2"': 0.00038276804434473694, '"MT-ND4"': 0.00037763508606354233, '"NDUFB10"': 0.00037583849770628377, '"MNS1"': 0.00037513197923332156, '"CEP63"': 0.0003744283522531029, '"TRIM44"': 0.0003741009205580315, '"CTNND1"': 0.00037305538183162547, '"BRD4"': 0.00037133059642590694, '"EFNA2"': 0.0003709151110211983, '"CMIP"': 0.0003695453225543253, 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0.0003331367020683582, '"APOOL"': 0.00033202494231379654, '"GPX4"': 0.0003305773146619669, '"CSTB"': 0.0003301412873022558, '"IRF2BPL"': 0.0003296894731237382, '"TK1"': 0.0003291832412886538, '"RPL27"': 0.00032892546428544216, '"NIN"': 0.0003275496568925339, '"CROCC"': 0.00032696519088910115, '"PHLDB2"': 0.00032646760839186926, '"LRRC59"': 0.00032588684776822016, '"SMARCB1"': 0.0003254954933337985, '"MT1E"': 0.0003251386791250482, '"ZNF132-DT"': 0.0003250979672949727, '"PPP1R14B"': 0.0003219544175655707, '"CCDC57"': 0.0003212249851497626, '"H2BC9"': 0.0003201920932333093, '"FAM162A"': 0.0003198407151453884, '"PGAM1"': 0.00031919823728083254, '"CEP55"': 0.0003161915821339287, '"ARHGDIA"': 0.00031554484076558455, '"MRPS33"': 0.00031520226851782727, '"HSPA4"': 0.0003148020579689929, '"STK11"': 0.00031317922905521183, '"MXRA5"': 0.0003115961761107638, '"SLC2A1"': 0.00030893384471637536, '"SEPTIN9"': 0.00030396917074621406, '"DGUOK"': 0.00030296180821768383, '"HSBP1"': 0.0003029427195952312, '"PSAP"': 0.0003014740532999153, '"TAOK3"': 0.00030056468368762725, '"PCBP1"': 0.0003000022249108906, '"C12orf75"': 0.0002985452833265202, '"CENPB"': 0.00029840625002589916, '"KMT5B"': 0.00029783092004277446, '"VIT"': 0.00029696719974604986, '"CD47"': 0.000295937963005207, '"ARHGEF39"': 0.0002953502008117917, '"RRAS"': 0.00029445818095959853, '"BACH1"': 0.0002928636370597901, '"CAV2"': 0.0002926402803572533, '"KRT5"': 0.00029163629004663483, '"HES1"': 0.0002911341877885281, '"NLE1"': 0.0002904738732685024, '"PLOD2"': 0.0002900159327974811, '"DNM2"': 0.00028945575618393056, '"FAM20B"': 0.00028766276854717024, '"IQCG"': 0.00028738962325380163, '"DTYMK"': 0.00028664663443152727, '"SHMT1"': 0.00028606633439946783, '"LMNB2"': 0.00028540840248478537, '"BET1"': 0.0002854080889311606, '"PIKFYVE"': 0.00028504496911256106, '"KRT17"': 0.00028464538374770997, '"LINC01304"': 0.00028454402653771405, '"SLC39A14"': 0.00028350105757825897, '"PPIG"': 0.0002832128297610758, 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0.00026506574230973195, '"RAB13"': 0.00026372224488181587, '"SLITRK5"': 0.00026363060191380184, '"RPL17"': 0.00026145875402767727, '"ANGPTL4"': 0.00026135565669849973, '"HSPBP1"': 0.00026036360593949796, '"NUMA1"': 0.000259040870571378, '"STX2"': 0.0002586463942085938, '"SEM1"': 0.00025821596013331867, '"SLC25A37"': 0.00025733338720660846, '"NAB1"': 0.0002565644288545512, '"PHLPP1"': 0.0002560782720651112, '"MT-ATP8"': 0.00025582455656797957, '"TAGLN2"': 0.000254102062919704, '"PLAAT3"': 0.0002533948103953058, '"GNB1"': 0.00025305897729395406, '"CAMSAP3"': 0.00025285418421405205, '"TWNK"': 0.0002527742012229306, '"MXI1"': 0.0002496008656244861, '"ZNF718"': 0.00024954128899077027, '"LRRIQ1"': 0.0002490962369947508, '"MCM4"': 0.0002479217286138264, '"WBP4"': 0.000247024420854593, '"PRDM2"': 0.00024625102647736507, '"PRPF31"': 0.000245900650555612, '"RAB5A"': 0.000245727197686686, '"PFKL"': 0.00024509095209725954, '"ANAPC16"': 0.0002449054930126537, '"LINC02367"': 0.00024342200862754806, 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0.00022800701572882518, '"EFNB2"': 0.00022728547652785288, '"DANT1"': 0.00022638805188288837, '"STT3A"': 0.00022422654083296034, '"PPL"': 0.00022280824260630555, '"TAF12"': 0.00022235481489265907, '"UBN2"': 0.00022205029148486666, '"RPL7A"': 0.00022081364688267282, '"MAP3K14"': 0.00022074583775865764, '"JUN"': 0.00022067201360735002, '"SOS1"': 0.00022059732799120424, '"NMD3"': 0.0002203244375751095, '"NEK2"': 0.00021979335492632786, '"YKT6"': 0.00021951594622034295, '"GIN1"': 0.0002188835486894249, '"CELSR1"': 0.00021786590724382545, '"TOP2B"': 0.00021775543250839133, '"STUB1"': 0.00021631056802937494, '"RAP2B"': 0.00021557553159727992, '"ODF2"': 0.00021555821310277582, '"GNB2"': 0.00021528723097577178, '"FBXO32"': 0.0002151450810590785, '"NFE2L2"': 0.0002149513281976769, '"KLF16"': 0.00021439626140812136, '"H2AZ2"': 0.00021336574963567214, '"MPHOSPH6"': 0.00021319063391082014, '"PSMD9"': 0.0002128965955794182, '"RANGAP1"': 0.00021253142110515857, '"DYNC2I2"': 0.00021193746359060876, 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0.00014930632015493645, '"CACTIN"': 0.0001491334435922437, '"MSANTD3"': 0.0001490383761172522, '"PRR15"': 0.00014827297878121777, '"COX8A"': 0.00014817704510606476, '"NACA4P"': 0.00014797309164687247, '"EEF1A2"': 0.000147831919833748, '"IGFBP7"': 0.00014781069821093247, '"FOXN3-AS1"': 0.00014747924933003224, '"CDC42EP1"': 0.0001473009747659587, '"TMEM238"': 0.00014721665603321108, '"HOXC13-AS"': 0.0001469121023727771, '"HIVEP3"': 0.00014671497421901727, '"TCF20"': 0.00014669718896807095, '"PCBD1"': 0.00014669492695102294, '"MED18"': 0.00014646207518966155, '"RGL2"': 0.00014596042815469962, '"DGUOK-AS1"': 0.0001454845037696547, '"CDC42BPA"': 0.0001454489489095823, '"LINC01666"': 0.00014526646640719654, '"BTBD7P1"': 0.000145134472644446, '"IPMK"': 0.0001450290991585605, '"TCEAL9"': 0.00014494015369892848, '"WHAMMP3"': 0.00014427154512712735, '"SPRYD4"': 0.00014379284498794594, '"COL6A3"': 0.00014365185016641896, '"SLC25A28"': 0.0001435953485596018, '"UGT1A7"': 0.0001434009624943753, '"ZBTB38"': 0.0001432257079387805, '"NUDT14"': 0.00014319795518086064, '"POLR3A"': 0.000143064757670291, '"FBXL17"': 0.00014298120261336877, '"FANCE"': 0.0001428659480758485, '"RAB2B"': 0.00014280249016388093, '"FRY"': 0.0001424879096884028, '"PALM3"': 0.00014232724239321431, '"CHCHD7"': 0.00014223689746741339, '"BICD1"': 0.00014211257706998222, '"SMDT1"': 0.00014204998914664227, '"ZBTB45"': 0.00014172908276723547, '"EPB41L2"': 0.00014116957814905927, '"NSMF"': 0.00014107067480810079, '"ZNF341"': 0.00014089099181445317, '"RAB31"': 0.00014066593303094224, '"YTHDF1"': 0.00014039134346719367, '"KIF16B"': 0.00014021658110190932, '"AGK"': 0.00014018992292080915, '"ZNF358"': 0.000139997291988734, '"BCL2L12"': 0.0001398891350738934, '"MAP7"': 0.00013977896300606187, '"MLLT6"': 0.00013977625484825124, '"ENTR1"': 0.00013970504058774652, '"EPB41L1"': 0.00013964520791177152, '"SFMBT1"': 0.00013939926774223904, '"PMVK"': 0.00013892533844142463, '"TCF19"': 0.0001387526894875243, '"TOLLIP"': 0.0001387481264159155, '"FARS2"': 0.00013874042621543696, '"FGF12"': 0.00013849370413761874, '"MACROH2A2"': 0.00013843042672545986, '"PPARA"': 0.0001383822420858464, '"UQCRHL"': 0.00013824814226107797, '"LRAT"': 0.0001378065417063106, '"EPPK1"': 0.00013755273657208256, '"MAST4"': 0.0001375255393880784, '"MCM6"': 0.00013699387077204835, '"SPINT1-AS1"': 0.00013591083365971222, '"NT5C"': 0.00013491372407668716, '"NUAK1"': 0.0001347850111246652, '"ERI1"': 0.00013406997792322223, '"EIF5AL1"': 0.00013388410844752068, '"RGPD4-AS1"': 0.00013373196245833238, '"LEO1"': 0.00013369965894821154, '"SLC1A5"': 0.00013280640609334722, '"SINHCAFP3"': 0.0001328044859655438, '"LARP7"': 0.00013279544580742015, '"SLC6A8"': 0.00013272122297906968, '"CUL4B"': 0.00013188720328651335, '"MRFAP1"': 0.00013181071769579965, '"FAM20C"': 0.00013178421636747436, '"CRBN"': 0.0001316174349324653, '"LINC01503"': 0.00013109535665441384, '"CBX4"': 0.00013007665825703584, '"CSTA"': 0.00012968801141404157, '"CIRBP"': 0.0001293075716925879, '"MGMT"': 0.0001289780742360211, '"FLOT1"': 0.00012876617843898846, '"LSM4"': 0.00012806581544119736, '"TMEM52B"': 0.00012781592178763432, '"TBC1D16"': 0.00012732167287889777, '"ADM"': 0.0001272428638717744, '"SNX18"': 0.0001266687430191914, '"TRMT5"': 0.00012631556550004463, '"RPL22L1"': 0.00012584043289891474, '"SECISBP2"': 0.00012502114117801338, '"DEPDC1B"': 0.0001248311720088767, '"WDR82"': 0.00012478520999293445, '"SYK"': 0.0001243584342056804, '"EIF3J-DT"': 0.0001242738966972122, '"ZFP3"': 0.00012425801112360326, '"CNPY2-AS1"': 0.000123978013359157, '"MTCO1P12"': 0.0001239066255511715, '"XRCC1"': 0.00012389818029954659, '"CMTM3"': 0.00012388457106531097, '"XPNPEP1"': 0.00012375380541634418, '"KCNG1"': 0.00012372234995197817, '"ZNF710"': 0.00012358647021590182, '"SLC30A6-DT"': 0.00012349671014544978, '"HMG20B"': 0.000123268499797269, '"SMAD3"': 0.0001230618451068284, '"HDDC3"': 0.00012302841142860176, '"RPA1"': 0.00012287760762013828, '"CPE"': 0.0001227372056490503, '"RSPH3"': 0.00012243236084508998, '"LIMS1"': 0.0001223283842012364, '"PSG2"': 0.0001221944594087437, '"CRYZL1"': 0.00012201525125862446, '"DTD1"': 0.00012201293947961133, '"SAP30-DT"': 0.00012195692598539647, '"ATN1"': 0.00012182387847957645, '"POLDIP2"': 0.00012180896215430489, '"MMP2"': 0.00012180600844963568, '"H2AX"': 0.00012174716463181668, '"WDR77"': 0.00012169362002452024, '"BMPR1B"': 0.00012160986674253551, '"SIGMAR1"': 0.00012159502584419396, '"DOP1A"': 0.00012139536228254638, '"PGLS"': 0.00012132219355948139, '"TIMP3"': 0.00012127401791918428, '"NAXD"': 0.00012118143245078909, '"HEY2"': 0.00012113206549610044, '"RBX1"': 0.00012110749400077944, '"PKD1L1"': 0.00012086419313913725, '"DNMT3A"': 0.0001208411670541617, '"CCDC168"': 0.00012083020629425094, '"RBFOX2"': 0.00012080630682677676, '"DNAJB2"': 0.00012075885175690466, '"SGSM2"': 0.00012064941414403926, '"PRPSAP2"': 0.00012056504461452058, '"TMEM52"': 0.00012048331810583885, '"TMEM80"': 0.00012043212378524098, '"HNRNPUL2"': 0.00012037412729576339, '"PPP2R1A"': 0.00012006915911628127, '"TAF10"': 0.00011973291807516789, '"WNT4"': 0.00011969610963587537, '"NIF3L1"': 0.0001195563151145438, '"SRI"': 0.00011951080167769256, '"DNPH1"': 0.00011942821694430839, '"TNFRSF12A"': 0.00011933424494054425, '"CASP6"': 0.00011926328241788483, '"PIH1D2"': 0.00011902823945175968, '"KLC2"': 0.00011878963253162813, '"MAP3K1"': 0.00011857786180624894, '"TAF13"': 0.00011831106736291184, '"SYNJ2"': 0.00011821252883104283, '"SNCG"': 0.00011806264171637302, '"MAP2"': 0.00011759969220945005, '"BDH2"': 0.00011731152727378876, '"AK1"': 0.0001172001200381172, '"MOCOS"': 0.00011712011847751899, '"DLG5"': 0.00011696086656731437, '"TRIM35"': 0.0001168588221742331, '"FBXO38"': 0.00011675847765401978, '"ARMC5"': 0.00011657601017039747, '"METTL5"': 0.00011625366907778021, '"PRR14L"': 0.00011613470364199224, '"HIGD1A"': 0.00011603144918974072, '"TUBA5P"': 0.00011579587111841948, '"AK4"': 0.00011578126010488499, '"GAS6-DT"': 0.00011566112644799607, '"CCDC167"': 0.00011530559316571126, '"PKP4"': 0.00011470211687179292, '"GHDC"': 0.00011466050736524017, '"LINC01186"': 0.00011451270473605318, '"ATP5MC2"': 0.00011443131422469909, '"LETM1"': 0.00011433749070673951, '"ZDHHC4"': 0.00011422613461722407, '"ZNF703"': 0.00011390678356827247, '"OVCH1-AS1"': 0.00011359786551073936, '"SMIM10L1"': 0.0001135831479855334, '"GFOD1"': 0.00011346673226563618, '"EFNA5"': 0.00011327538044139139, '"IER3IP1"': 0.00011325837021083573, '"RETREG2"': 0.00011314890103817645, '"MPDU1"': 0.000113112189889286, '"NTAN1"': 0.00011274401708269495, '"ST14"': 0.00011261287661263093, '"LGALS1"': 0.00011252962213845822, '"SPRYD3"': 0.00011230633004227786, '"MED25"': 0.00011087960224140463, '"HSBP1L1"': 0.00011085081070646822, '"SNRPA"': 0.00011083798689737334, '"ARID3A"': 0.00011049910756245505, '"ZCCHC3"': 0.0001099889957199951, '"CLIP2"': 0.0001098775902225552, '"PLEKHG3"': 0.00010981557525246879, '"HRAS"': 0.00010962081785610867, '"FBXO48"': 0.00010949929642405008, '"C3orf14"': 0.00010837221610347729, '"REST"': 0.00010813817306530907, '"MTUS1"': 0.00010800188495411266, '"NARF"': 0.00010792631277504738, '"RNF170"': 0.00010740941753471206, '"LINC02484"': 0.00010735008612004811, '"MAD2L1"': 0.00010693777681733357, '"RNF187"': 0.00010692729700516039, '"H19"': 0.00010671360547595095, '"ZDHHC12"': 0.00010614621519188457, '"GNG5"': 0.00010544027129291479, '"FZD8"': 0.00010514314587448336, '"BRI3"': 0.0001050461275545114, '"CAPG"': 0.00010467188362033202, '"RP9"': 0.00010462512019264914, '"LAMA5"': 0.00010448966196152971, '"GADD45A"': 0.00010441843012304894, '"THRB"': 0.00010437719178803204, '"MTND1P23"': 0.00010413790521401813, '"ZNF318"': 0.00010387724239624412, '"IFI27L2"': 0.00010335290004919785, '"C16orf95-DT"': 0.00010329651656062649, '"PRR34-AS1"': 0.00010270907350390408, '"RAD54L2"': 0.00010139075859807184, '"ZBTB2"': 0.0001006425024156871, '"RNF215"': 0.00010040176185357642, '"ZNF317"': 0.0001003678657856253, '"ARHGEF26"': 9.988335518334424e-05, '"AP1S3"': 9.946327224838155e-05, '"CDK2AP2"': 9.897910424101781e-05, '"GEN1"': 9.854326631327114e-05, '"EPS8L2"': 9.785234234179494e-05, '"GNAS"': 9.549469659576559e-05, '"PNPLA3"': 9.537506598842957e-05, '"DRAP1"': 9.533072659306056e-05, '"DIP2C"': 9.519107538117833e-05, '"AGRN"': 9.452284901155599e-05, '"MPPE1"': 9.437399436574548e-05, '"FBXL19"': 9.418752809676265e-05, '"MVK"': 9.4012739939234e-05, '"ARMC2"': 9.396286468634006e-05, '"WDR54"': 9.38439734635563e-05, '"BOK"': 9.383312088249547e-05, '"ITGA3"': 9.366173383642729e-05, '"MCM3AP"': 9.351912657517495e-05, '"DPCD"': 9.34793513790509e-05, '"ZDHHC8"': 9.336464330225033e-05, '"C16orf74"': 9.334220571667528e-05, '"KRT4"': 9.330971957907539e-05, '"GPR153"': 9.330841713371325e-05, '"NUP62"': 9.326454191554115e-05, '"CBWD3"': 9.326221874276708e-05, '"AMDHD2"': 9.299911928330488e-05, '"ZNF407-AS1"': 9.29953829044278e-05, '"MAPK8"': 9.297757414473726e-05, '"LINC01772"': 9.294008961831871e-05, '"TRAF4"': 9.278899564899244e-05, '"NFKBIL1"': 9.274584282351476e-05, '"SLC16A4"': 9.273281510590135e-05, '"OGDH"': 9.264971232542914e-05, '"DCTN2"': 9.258327043227085e-05, '"C19orf81"': 9.255604315267097e-05, '"UIMC1"': 9.251825755920593e-05, '"FAM126B"': 9.228468538102751e-05, '"MAN2B1"': 9.225746128548726e-05, '"EEF2K"': 9.219978767173361e-05, '"ULK2"': 9.201895367950006e-05, '"LTBP3"': 9.200404208758027e-05, '"GNAI2"': 9.185658590719054e-05, '"NAP1L1P1"': 9.18020105045707e-05, '"ARHGEF7"': 9.17305165182919e-05, '"YY1AP1"': 9.164002596833764e-05, '"DNHD1"': 9.16282587710843e-05, '"NRBP1"': 9.162464924049047e-05, '"TMTC4"': 9.141718456217527e-05, '"KBTBD7"': 9.137359108924135e-05, '"TBC1D22A"': 9.13171523459363e-05, '"ZNF195"': 9.126807884472676e-05, '"NUDT8"': 9.116408509361217e-05, '"KCTD15"': 9.112088604982712e-05, '"RPL21P34"': 9.103281261857495e-05, '"H2BC4"': 9.08624651646754e-05, '"BIK"': 9.079884249666155e-05, '"XYLB"': 9.079397849444085e-05, '"PRELID2"': 9.071881766862993e-05, '"IVL"': 9.069718767802659e-05, '"JMJD6"': 9.065484945897635e-05, '"WARS2"': 9.058536644192925e-05, '"KHK"': 9.053808014465877e-05, '"ZFP36L1"': 9.053550717329228e-05, '"ZNF184"': 9.046191993691752e-05, '"ZNF146"': 9.041372074579939e-05, '"CLIC4"': 9.027967857536168e-05, '"PSMA5"': 9.024408740354607e-05, '"C1QTNF6"': 9.022503324124382e-05, '"NCK1"': 9.012825529678355e-05, '"MELTF-AS1"': 9.001065602930454e-05, '"CDK14"': 9.000431339581138e-05, '"ULK1"': 8.998135032604948e-05, '"HNRNPCP3"': 8.996733199670262e-05, '"ZFP30"': 8.994411863465061e-05, '"OTULINL"': 8.992989700466958e-05, '"MTND4P12"': 8.973838764339724e-05, '"TONSL"': 8.970719819897505e-05, '"HMGB1P20"': 8.967634085099488e-05, '"C4orf46"': 8.955869744752154e-05, '"MAZ"': 8.940887599512761e-05, '"PCED1A"': 8.939319159719028e-05, '"LINC01234"': 8.934882361256831e-05, '"HNF4A"': 8.930609842821351e-05, '"BIN3"': 8.9190330451241e-05, '"TRIM8"': 8.91665588697229e-05, '"BRAT1"': 8.911990481530444e-05, '"LINC02298"': 8.905551809505478e-05, '"SDAD1P1"': 8.897199669848962e-05, '"QSOX1"': 8.87984596372198e-05, '"ZFC3H1"': 8.875569642591673e-05, '"SLC25A46"': 8.871991098156979e-05, '"AKR1A1"': 8.853578914080392e-05, '"SH3RF2"': 8.851048330236139e-05, '"MAFF"': 8.84547475160065e-05, '"CARM1"': 8.822669827585198e-05, '"CLEC11A"': 8.808529884609504e-05, '"MID1IP1"': 8.802873531247926e-05, '"PTPN6"': 8.785118994560345e-05, '"ZDHHC7"': 8.756493443309609e-05, '"TRIOBP"': 8.747282642953206e-05, '"OBSCN"': 8.746916506751959e-05, '"AKT1S1"': 8.724663606065393e-05, '"EFCAB1"': 8.716354536271993e-05, '"ILRUN-AS1"': 8.715901949213125e-05, '"KLHL7"': 8.700299848757052e-05, '"GPM6B"': 8.698677322116632e-05, '"SRGAP2"': 8.678059231197981e-05, '"PFKFB3"': 8.672914623821159e-05, '"ADARB1"': 8.670284664750243e-05, '"HAAO"': 8.651706982541966e-05, '"DOP1B"': 8.639707348357664e-05, '"FBXW5"': 8.624324162338105e-05, '"ERRFI1"': 8.620366717701333e-05, '"GSS"': 8.604435115858415e-05, '"TCF3"': 8.594210906178716e-05, '"NRAV"': 8.57637332589008e-05, '"SPA17"': 8.557998743979328e-05, '"HAUS7"': 8.548991916877292e-05, '"DCAF6"': 8.54453488669986e-05, '"MT-TS1"': 8.537177289006246e-05, '"C1orf21"': 8.536107656524565e-05, '"PDXK"': 8.529032647898994e-05, '"CCDC136"': 8.46627924376799e-05, '"DPM3"': 8.456120550108767e-05, '"FAM76B"': 8.440357974387431e-05, '"RAVER1"': 8.43333666977683e-05, '"SLITRK2"': 8.432434236156018e-05, '"UCA1"': 8.426754378573085e-05, '"ZBED4"': 8.420926150463098e-05, '"TSPO"': 8.395136998923402e-05, '"FBXO8"': 8.372710180489269e-05, '"CDK5RAP2"': 8.329479166393283e-05, '"NEDD9"': 8.325454635371105e-05, '"ATP13A2"': 8.306880154440233e-05, '"RPSAP48"': 8.269354240163232e-05, '"ECH1"': 8.250584298536548e-05, '"PSD3"': 8.250001086416508e-05, '"CRACR2A"': 8.248129243207393e-05, '"PDIA5"': 8.247137671078356e-05, '"GCAT"': 8.244914363007675e-05, '"SLMAP"': 8.24203088458312e-05, '"NRSN2-AS1"': 8.232651208261943e-05, '"GMPR2"': 8.231011255017882e-05, '"UBE2C"': 8.195426107289373e-05, '"CCNI"': 8.170099422482318e-05, '"SUCLG2"': 8.164369103150995e-05, '"LINC01962"': 8.136506426051155e-05, '"TMEM40"': 8.116897273546079e-05, '"SLC2A11"': 8.111825722425076e-05, '"SBNO2"': 8.109280582853116e-05, '"MINDY2"': 8.107562293231969e-05, '"ZNF280B"': 8.087495790391859e-05, '"ID1"': 8.070257408420093e-05, '"FDXACB1"': 8.052448138147666e-05, '"TPD52L1"': 8.042261021624678e-05, '"MRPS2"': 8.02415043428281e-05, '"MBD3"': 7.835043757826459e-05, '"SRC"': 7.825578114182603e-05, '"ARHGAP42"': 7.791831712904143e-05, '"SMIM4"': 7.765906733590497e-05, '"RAB20"': 7.720497080597152e-05, '"NAT14"': 7.713994307016983e-05, '"GTF2IRD1"': 7.632116194683131e-05, '"SENP7"': 7.579287975959559e-05, '"PRPF40B"': 7.546218056774426e-05, '"NDUFA2"': 7.450657251682234e-05, '"HES4"': 7.413211363751802e-05, '"ZMYND8"': 7.271256696472562e-05, '"AP1M1"': 7.258502408611888e-05, '"ELP2"': 7.205550696412233e-05, '"OXLD1"': 7.039251770691914e-05, '"CNTRL"': 6.995742593455304e-05, '"CREB3L2"': 6.98264699850761e-05, '"RAB11FIP5"': 6.955333745794596e-05, '"ZKSCAN2"': 6.878740313801181e-05, '"FCHO2"': 6.852609460962806e-05, '"PLEKHA4"': 6.821962279061105e-05, '"MAN1A1"': 6.769968451341317e-05, '"REXO1"': 6.735276321343187e-05, '"DUSP9"': 6.606268109354551e-05, '"CPEB1"': 6.550902021173581e-05, '"PPTC7"': 6.517269527060283e-05, '"UBE2D1"': 6.419259069040781e-05, '"GDE1"': 6.414558054956844e-05, '"TBC1D19"': 6.342147228066472e-05, '"ACSF3"': 6.315991487296738e-05, '"WDR53"': 6.304812064367445e-05, '"GLCCI1"': 6.295141819513206e-05, '"SMC6"': 6.291751991772982e-05, '"CRLS1"': 6.286933639821965e-05, '"B3GAT2"': 6.283655877178698e-05, '"RAB11FIP4"': 6.28041367817532e-05, '"LRRC20"': 6.270967094516001e-05, '"TKFC"': 6.270581114430525e-05, '"GALM"': 6.266151875520278e-05, '"ARL17B"': 6.264998685028945e-05, '"MT-TL1"': 6.254912853770947e-05, '"STC1"': 6.252993350819284e-05, '"CEP120"': 6.247136640266256e-05, '"DNA2"': 6.24534067763113e-05, '"EFNB1"': 6.244710012159677e-05, '"SOX11"': 6.242323751182444e-05, '"MORC3"': 6.238748438420596e-05, '"GJD2"': 6.236237406582099e-05, '"TMEM70"': 6.234068304902647e-05, '"DTWD2"': 6.230784566884204e-05, '"TAF1A"': 6.230677329662045e-05, '"ACP5"': 6.229876127591114e-05, '"MT-TM"': 6.223803261864425e-05, '"MAML2"': 6.221205038908472e-05, '"ZNF629"': 6.215935654631888e-05, '"C10orf88"': 6.213634132089965e-05, '"C18orf32"': 6.21299162160354e-05, '"TMEM121"': 6.211515336084182e-05, '"LINC01902"': 6.209679738285713e-05, '"NDST1"': 6.207642533216346e-05, '"WBP2"': 6.207104325025327e-05, '"PI4KB"': 6.20463679873449e-05, '"AJAP1"': 6.204235551594282e-05, '"DYNC2I1"': 6.203507185454723e-05, '"UAP1L1"': 6.201410971673761e-05, '"ANKMY2"': 6.19957159087736e-05, '"BNC1"': 6.199137844043613e-05, '"UBQLN2"': 6.19481657566068e-05, '"AMZ2P1"': 6.19328927859059e-05, '"ESCO1"': 6.191985714789964e-05, '"BOLA1"': 6.191872467844835e-05, '"FHL2"': 6.189666215414523e-05, '"SELENOO"': 6.188992894479311e-05, '"RARG"': 6.187705079904438e-05, '"MRPS6"': 6.18535566035664e-05, '"SLC2A8"': 6.183972970835101e-05, '"CCDC51"': 6.181735674998877e-05, '"NUPR2"': 6.179417556632854e-05, '"GNAS-AS1"': 6.179167293830461e-05, '"VAV2"': 6.177597904971852e-05, '"MAML1"': 6.175008962479365e-05, '"CHMP6"': 6.170964995348365e-05, '"SLC9A3"': 6.16639425579093e-05, '"HES2"': 6.16551856376718e-05, '"PLAC8"': 6.16354111674283e-05, '"MAB21L3"': 6.162665712060108e-05, '"FBXO33"': 6.161556031186621e-05, '"ERG"': 6.161307197737395e-05, '"ZNF213"': 6.157049436610562e-05, '"NCK2"': 6.156944457323427e-05, '"MDFI"': 6.153371437542215e-05, '"DANT2"': 6.139037795767708e-05, '"SDHB"': 6.13705348866631e-05, '"THNSL1"': 6.136646771293659e-05, '"SLC25A1"': 6.13116869297305e-05, '"ATXN2L"': 6.12758459585575e-05, '"FOXD1"': 6.126878573302177e-05, '"PRKAA2"': 6.125051505812228e-05, '"CREB1"': 6.121211402467571e-05, '"FOXP4"': 6.121084302395088e-05, '"HOXA4"': 6.114213129118707e-05, '"CACNB3"': 6.108932184770789e-05, '"GATD1"': 6.106746628652511e-05, '"ZNF324"': 6.103843755566762e-05, '"MCEE"': 6.102841688792749e-05, '"MAP3K13"': 6.102511607437324e-05, '"TRAK1"': 6.1003790509851424e-05, '"RGL3"': 6.0961164246631705e-05, '"PTPN21"': 6.091914399459566e-05, '"TFPI2"': 6.0834197871310144e-05, '"IFI35"': 6.080491796044056e-05, '"CASK"': 6.076256377970486e-05, '"TBC1D10A"': 6.0653328338185786e-05, '"ARHGAP22"': 6.065231977676447e-05, '"IDH3G"': 6.06214433623923e-05, '"SLC25A51P4"': 6.0586340084018745e-05, '"SHFL"': 6.054618219299507e-05, '"SORBS1"': 6.053700524586441e-05, '"FAM200B"': 6.05358000052254e-05, '"ZCCHC9"': 6.051428769673674e-05, '"PDLIM4"': 6.042222670955944e-05, '"ZNF23"': 6.040698148302807e-05, '"LINC02511"': 6.040483882773931e-05, '"SLC26A6"': 6.033408873079233e-05, '"RCHY1"': 6.029262932133991e-05, '"MLXIP"': 6.019663371789788e-05, '"SH3BGRL"': 6.013900865656445e-05, '"CUEDC2"': 6.0119157739467706e-05, '"TMEM79"': 6.0115023850737286e-05, '"CAMKK1"': 6.010584563838184e-05, '"DYNLT3"': 5.993380253323903e-05, '"SMOX"': 5.9931614804490405e-05, '"TSEN54"': 5.990085749895519e-05, '"CASP1"': 5.989851378091027e-05, '"PAX5"': 5.982424762202014e-05, '"ERG28"': 5.9796373755806755e-05, '"SPINK5"': 5.974407336716116e-05, '"MLLT3"': 5.973392657023115e-05, '"RAB36"': 5.9730494134032546e-05, '"LSP1P4"': 5.9674279567777665e-05, '"ITPKC"': 5.9662878334016236e-05, '"ARHGEF18"': 5.964834371784061e-05, '"PLSCR1"': 5.9623765912243914e-05, '"SNAPC3"': 5.9542809175929183e-05, '"CES1"': 5.948780322499299e-05, '"CPTP"': 5.934840528358891e-05, '"RBBP8NL"': 5.931942797026107e-05, '"ETAA1"': 5.9305831058452363e-05, '"MAP1A"': 5.929537620903034e-05, '"ARFGEF3"': 5.9251013515695906e-05, '"NCAM1"': 5.924937132959457e-05, '"CARF"': 5.920834520943335e-05, '"BORCS6"': 5.9160430401837444e-05, '"ABCA2"': 5.9123930284474484e-05, '"OR10K1"': 5.907665255606751e-05, '"MESP1"': 5.906310315645454e-05, '"MAPK14"': 5.9042755025441726e-05, '"GMPPA"': 5.9032877345232116e-05, '"C4orf48"': 5.896542170047349e-05, '"POLR3GL"': 5.8905568534067365e-05, '"SLC25A23"': 5.8787266250351334e-05, '"HHLA3"': 5.872328834480871e-05, '"RABGGTA"': 5.8683816171122806e-05, '"FAM83A-AS1"': 5.8665064289863196e-05, '"MAFK"': 5.8428096239386195e-05, '"NRGN"': 5.841848058038832e-05, '"ROM1"': 5.8367224261962115e-05, '"COX14"': 5.820507180672444e-05, '"PLCXD2"': 5.817013426705993e-05, '"KCTD1"': 5.816711033595957e-05, '"C15orf39"': 5.815089375475331e-05, '"SOX15"': 5.814169545124565e-05, '"LDOC1"': 5.8029239243266626e-05, '"MT-TY"': 5.795265298372581e-05, '"BTBD6"': 5.789100350390686e-05, '"NKX3-1"': 5.78748424098743e-05, '"MAPK12"': 5.7823170486586374e-05, '"CTF1"': 5.778624238274635e-05, '"LSM14A"': 5.7771771724496345e-05, '"MT1F"': 5.7754942750015304e-05, '"TCP11L1"': 5.773923608220691e-05, '"ATP1A1-AS1"': 5.771721183399942e-05, '"SHKBP1"': 5.77169001181963e-05, '"PDPK1"': 5.759046060520946e-05, '"CDK19"': 5.755012848469933e-05, '"NEFL"': 5.745426326072403e-05, '"TTC3P1"': 5.7405059444499206e-05, '"KRT16"': 5.739823699377112e-05, '"LRRC23"': 5.734955982577926e-05, '"RNF10"': 5.682441153201165e-05, '"ARAF"': 5.6616105687641325e-05, '"ZNF628"': 5.6521054639193726e-05, '"FAM107B"': 5.647497425557699e-05, '"FBXO42"': 5.6473424519793165e-05, '"LINC01151"': 5.63174776862427e-05, '"UNC45A"': 5.627341420474621e-05, '"SH3BP1"': 5.6236136791475264e-05, '"DARS1-AS1"': 5.6152204052326285e-05, '"PHRF1"': 5.6087879022148913e-05, '"MKNK2"': 5.605871993047833e-05, '"COL5A1"': 5.600710080861485e-05, '"FAM107A"': 5.5823372870991154e-05, '"TXNRD2"': 5.579579395965451e-05, '"FBRSL1"': 5.574964366573086e-05, '"COMMD6"': 5.5528521086723644e-05, '"IRAK1"': 5.5340276202930646e-05, '"PIAS2"': 5.5283166099638735e-05, '"PBX4"': 5.5255669171624944e-05, '"DOCK6"': 5.520646326120147e-05, '"TMEM179B"': 5.510301684826954e-05, '"TRDN"': 5.499130078398796e-05, '"CSRP1"': 5.493681507732156e-05, '"ZNF524"': 5.486942816072799e-05, '"SWSAP1"': 5.478706949185233e-05, '"PFKP"': 5.4786182558063115e-05, '"KIAA2012-AS1"': 5.4609644085645026e-05, '"TPRA1"': 5.440291301976687e-05, '"PPP1R21"': 5.3181358021448735e-05, '"MBD2"': 5.306063350111619e-05, '"FAM83A"': 5.2939507503814055e-05, '"TLE3"': 5.2460817862109684e-05, '"ZNF598"': 5.203381822063371e-05, '"PBXIP1"': 5.1884974062498954e-05, '"AP1S2"': 5.1879346980240434e-05, '"MSR1"': 5.182173476771968e-05, '"ARL9"': 5.1771285097556805e-05, '"APPL1"': 5.172077647851101e-05, '"IL6R"': 5.150016914722894e-05, '"MRPL14"': 5.14160622405891e-05, '"CNOT6L"': 5.141033754793486e-05, '"FAH"': 5.1402612514431645e-05, '"STYX"': 5.127209871324254e-05, '"ACVR2B"': 5.0134221353704604e-05, '"BASP1"': 4.9993676498897435e-05, '"S100A13"': 4.961697008038483e-05, '"RAB11B"': 4.924179450321743e-05, '"CAPZB"': 4.92223013687409e-05, '"L3MBTL2"': 4.8303424164768184e-05, '"IQCC"': 4.745958725512102e-05, '"THOC7"': 4.7424718918545245e-05, '"YEATS4"': 4.719017127110547e-05, '"FADS2"': 4.702924369263588e-05, '"RHBDF1"': 4.7001993865170913e-05, '"CLDN11"': 4.676128879229621e-05, '"KCTD11"': 4.6708929105269914e-05, '"THAP2"': 4.654101550665846e-05, '"PDLIM3"': 4.635938788100662e-05, '"SPATC1L"': 4.544095628159059e-05, '"UBL4A"': 4.5222056176424184e-05, '"JUND"': 4.505568501435231e-05, '"TRIB2"': 4.476269763723625e-05, '"TUBA1C"': 4.2335323186441e-05, '"LAGE3"': 4.215189154818845e-05, '"FAM120C"': 4.12377641566558e-05, '"C19orf54"': 4.1136700439214036e-05, '"HSPA2"': 4.064502975279487e-05, '"CRNDE"': 4.048508953504771e-05, '"IFRD2"': 4.044447861914603e-05, '"TEX9"': 4.024540817475344e-05, '"PLD5"': 4.0134435718932945e-05, '"NEK8"': 3.9996335939051426e-05, '"TRAPPC2B"': 3.968949548980198e-05, '"PATZ1"': 3.946592595662319e-05, '"DLK2"': 3.941197206473911e-05, '"HEY1"': 3.898743070064991e-05, '"FUOM"': 3.876086589592319e-05, '"NEK1"': 3.875733890309952e-05, '"ACSL4"': 3.8737407247679866e-05, '"MIXL1"': 3.853872713817447e-05, '"AKR7A2"': 3.817040327653609e-05, '"SLC38A10"': 3.701310097673099e-05, '"TANGO2"': 3.184660463598838e-05, '"TRIM52-AS1"': 3.1831218587225815e-05, '"SLC52A1"': 3.1800919226727946e-05, '"WNT7A"': 3.1784736627005717e-05, '"ZNRF1"': 3.172890948758356e-05, '"ZNF462"': 3.16690808168254e-05, '"YPEL2"': 3.1641683443173715e-05, '"SMCO4"': 3.164081442282183e-05, '"SMIM29"': 3.163110086216561e-05, '"TMEM126A"': 3.162168699276014e-05, '"SH2B1"': 3.159957137361181e-05, '"POLE2"': 3.159497081160649e-05, '"SPDYE3"': 3.1575704888676706e-05, '"TMEM231"': 3.156842835337538e-05, '"SH3BGRL2"': 3.15658551269066e-05, '"SYT7"': 3.156428893601188e-05, '"ZNF25"': 3.156341769755613e-05, '"ZNF250"': 3.155770279395568e-05, '"SURF1"': 3.155655126856665e-05, '"TRG-AS1"': 3.154584388772286e-05, '"CCS"': 3.153109562692186e-05, '"NIPSNAP3A"': 3.1521872068967405e-05, '"GTF3C5"': 3.151684674209403e-05, '"RAD9A"': 3.151474406486248e-05, '"CCN2"': 3.1511062572667456e-05, '"TIAM2"': 3.1509561722928e-05, '"SH3D21"': 3.150174250746017e-05, '"HSP90AA4P"': 3.149373207634992e-05, '"PTPRB"': 3.149077865726821e-05, '"CXCL8"': 3.148804886559135e-05, '"LYPD1"': 3.1473749275835016e-05, '"LINC02870"': 3.146561338471396e-05, '"IL4R"': 3.146549650780264e-05, '"TMEM250"': 3.146218936565154e-05, '"LINC02273"': 3.1459769139379985e-05, '"ANKRD28"': 3.145523973714549e-05, '"UBE2I"': 3.1454749470299624e-05, '"GAS8"': 3.143876022906677e-05, '"RASSF10"': 3.143473099629647e-05, '"LRRC3"': 3.14313311525607e-05, '"CSPG4P12"': 3.1429807454485314e-05, '"ASB7"': 3.1427412888917564e-05, '"LINC01405"': 3.1419968239907344e-05, '"MTCO1P40"': 3.14145930218571e-05, '"PTPRU"': 3.1412513785616946e-05, '"TP53I13"': 3.1411291333892586e-05, '"WAC-AS1"': 3.14100483209892e-05, '"PRECSIT"': 3.140608783392842e-05, '"HEBP1"': 3.1404116451853585e-05, '"TINAGL1"': 3.1403683725002644e-05, '"ROR2"': 3.139462092376611e-05, '"DOCK9"': 3.1390405217945606e-05, '"ZFHX3"': 3.1382519691983544e-05, '"ZBTB47"': 3.1379583631031686e-05, '"PITPNM1"': 3.1379162027395365e-05, '"KLHL24"': 3.13771754540928e-05, '"LATS2"': 3.137674422644553e-05, '"PTRHD1"': 3.137364911985921e-05, '"LINC01687"': 3.1369742940737465e-05, '"PDE8A"': 3.1364170948357595e-05, '"PCIF1"': 3.135689493218926e-05, '"GATA3"': 3.135395894898744e-05, '"CORO7"': 3.134572108084446e-05, '"RTL6"': 3.134089484715586e-05, '"CRPPA"': 3.133309280965706e-05, '"CCDC92"': 3.132961190372491e-05, '"SREK1IP1P1"': 3.132837689891087e-05, '"ALPK1"': 3.1323745615984534e-05, '"IKBKE"': 3.132222417272333e-05, '"BOLA3-AS1"': 3.131877048445988e-05, '"BLOC1S6P1"': 3.131859732125571e-05, '"RNPEPL1"': 3.1313434636187355e-05, '"TBC1D20"': 3.131167386728794e-05, '"OVOL1"': 3.1309045657718194e-05, '"INPP5E"': 3.1308484191392485e-05, '"ADAM15"': 3.129822394126764e-05, '"PRKCH"': 3.128802629988007e-05, '"ZBTB10"': 3.127289824692753e-05, '"CUEDC1"': 3.127150985161103e-05, '"IQCH-AS1"': 3.126688661242637e-05, '"ZNF165"': 3.126472751430708e-05, '"LINC02582"': 3.126166816706608e-05, '"SREBF1"': 3.126116755591601e-05, '"CBWD6"': 3.125698238771557e-05, '"HAGLR"': 3.125632921649632e-05, '"ZNF74"': 3.123722971477788e-05, '"FOXJ2"': 3.1233108072919473e-05, '"NUP93"': 3.123196116532354e-05, '"LINC01931"': 3.1229500809740394e-05, '"SNHG19"': 3.1226553969830934e-05, '"C16orf95"': 3.1222842415760854e-05, '"MOV10"': 3.122117822399156e-05, '"MRPS36"': 3.122069598192496e-05, '"TPRG1"': 3.1220483175010557e-05, '"VPS9D1"': 3.121689491395696e-05, '"HLA-DPB1"': 3.121422489186762e-05, '"UCKL1"': 3.1210324501078516e-05, '"GBP1"': 3.120029294046544e-05, '"IGFL2-AS1"': 3.119905152860885e-05, '"PPP1R13L"': 3.119653323480991e-05, '"VEGFB"': 3.119444866369337e-05, '"ABT1"': 3.119310453921986e-05, '"FASTKD5"': 3.11925436776711e-05, '"C1orf112"': 3.1191975854972655e-05, '"CTHRC1"': 3.1189431493083616e-05, '"C14orf132"': 3.1188952116243886e-05, '"POLD1"': 3.1182035217384836e-05, '"LZTR1"': 3.118200169466327e-05, '"ATXN7L2"': 3.1179984279869775e-05, '"CEACAM19"': 3.1179275240328116e-05, '"IFITM10"': 3.117906834992552e-05, '"TCF7L1"': 3.1173201739162215e-05, '"CRACDL"': 3.116755391324157e-05, '"MUC4"': 3.116475969647453e-05, '"C20orf96"': 3.116364363928723e-05, '"PRRX2"': 3.1161726709034815e-05, '"HMGCS1"': 3.115717823834771e-05, '"FYN"': 3.115448413257823e-05, '"PRR14"': 3.115173709819811e-05, '"TAF1C"': 3.114874030099153e-05, '"RAPGEF3"': 3.114798379395685e-05, '"TRAFD1"': 3.1129382373552505e-05, '"LPAR4"': 3.112755068173907e-05, '"PKIB"': 3.112021155415624e-05, '"CAPN1"': 3.111890645360715e-05, '"PER1"': 3.111717658413274e-05, '"GKAP1"': 3.1107652411522286e-05, '"ZRANB1"': 3.110583113625266e-05, '"XKR8"': 3.110197697345216e-05, '"WDR74"': 3.110159345669508e-05, '"FAM189B"': 3.110140090958314e-05, '"NCOA1"': 3.1097547269982143e-05, '"GLIPR1"': 3.109466096487061e-05, '"TCAF1"': 3.109102595352327e-05, '"DVL1"': 3.109016362129162e-05, '"TOMM5"': 3.108869076758613e-05, '"ARVCF"': 3.108362341665337e-05, '"TDRKH-AS1"': 3.1082632472907216e-05, '"RHOXF2B"': 3.107896506897482e-05, '"CHST5"': 3.1078089531291394e-05, '"TBC1D22A-AS1"': 3.1077277195177965e-05, '"EPHX1"': 3.107648549288519e-05, '"HERC1"': 3.1068233963217785e-05, '"KIF26A"': 3.1057522645979905e-05, '"VDR"': 3.105336663170316e-05, '"DUSP23"': 3.105230990579142e-05, '"CASC2"': 3.104873696316948e-05, '"GABPA"': 3.1048046265533835e-05, '"CITED2"': 3.1047079664272055e-05, '"ZNF446"': 3.1046895470726894e-05, '"DHCR7"': 3.104664175606624e-05, '"UBA3"': 3.103859645938441e-05, '"E2F1"': 3.103711176055428e-05, '"PISD"': 3.103679789551824e-05, '"RMI2"': 3.103118091198665e-05, '"METTL25B"': 3.102986756278915e-05, '"SH3BP5L"': 3.102869737310251e-05, '"IPO13"': 3.102060710713725e-05, '"LMF2"': 3.1015680160042526e-05, '"ZNF268"': 3.1013452662185624e-05, '"HILPDA"': 3.101332985154584e-05, '"PDE6D"': 3.100745724684936e-05, '"MRPL45"': 3.100648038790894e-05, '"BEND6"': 3.1005435303413065e-05, '"MANBA"': 3.1004057942422585e-05, '"TMCO6"': 3.100173611115658e-05, '"TIGD1"': 3.0995679826947846e-05, '"RPL21P10"': 3.099220954743577e-05, '"GIPC1"': 3.09918585599888e-05, '"TMEM102"': 3.09890972064233e-05, '"NRBP2"': 3.097919107628416e-05, '"KRT18P59"': 3.0975834579669405e-05, '"TMEM256"': 3.097286888047438e-05, '"ITGB8-AS1"': 3.0961798152208466e-05, '"SNAP47"': 3.096086226458333e-05, '"MMAA"': 3.0957669547741884e-05, '"JAKMIP3"': 3.095757664422293e-05, '"GAS2L1"': 3.095198511630811e-05, '"SPATA2"': 3.0951285767607124e-05, '"FOXD2"': 3.0948765264222e-05, '"ALDH3B1"': 3.094031958215405e-05, '"TASOR"': 3.093810210600065e-05, '"GSK3A"': 3.093725684801391e-05, '"HOXC13"': 3.0921600341511886e-05, '"DPPA2"': 3.092033855740853e-05, '"NOP10"': 3.091138713533822e-05, '"ALS2CL"': 3.091109608147952e-05, '"WWC1"': 3.090702644083731e-05, '"MEGF6"': 3.090683472741623e-05, '"OPN3"': 3.090326378429516e-05, '"CIAO2A"': 3.09022242678701e-05, '"C19orf44"': 3.0900327265612856e-05, '"N4BP2L2-IT2"': 3.089980784545247e-05, '"PGBD2"': 3.089476205511272e-05, '"CMTM4"': 3.089408106866767e-05, '"GDI1"': 3.0892389288386915e-05, '"UQCRB-AS1"': 3.0891360582086955e-05, '"AAGAB"': 3.0891007471415914e-05, '"RAB35"': 3.0886261369693015e-05, '"PIP4P2"': 3.0882153209682456e-05, '"LINC02057"': 3.087698672853315e-05, '"CCDC88B"': 3.0875207425897955e-05, '"DBF4B"': 3.086090369038161e-05, '"MIR210HG"': 3.085806891816116e-05, '"TGFB1I1"': 3.085075382952701e-05, '"POLR2H"': 3.084861610297278e-05, '"SIRT5"': 3.084656910818693e-05, '"SLC4A2"': 3.084399710854188e-05, '"ANOS1"': 3.082419771521689e-05, '"NLGN2"': 3.081882933625339e-05, '"TUBD1"': 3.0816733191394565e-05, '"PLCG1"': 3.0802620108570674e-05, '"CCDC9B"': 3.080133666864222e-05, '"PCOLCE"': 3.079975674128389e-05, '"DMD"': 3.079808679880644e-05, '"MORN1"': 3.0794113247668056e-05, '"RHNO1"': 3.079092579234358e-05, '"BRSK2"': 3.078458284889232e-05, '"METAP1D"': 3.078359772727427e-05, '"ZNF8-DT"': 3.0782558730400004e-05, '"CSRNP1"': 3.07774323688368e-05, '"MCRIP1"': 3.0773478878554044e-05, '"SNAPC1"': 3.076973610736256e-05, '"TTC28"': 3.0750505022295456e-05, '"TNNT1"': 3.0746735015950095e-05, '"CTBP1"': 3.074649026638174e-05, '"SAMD4B"': 3.074268290557357e-05, '"ISOC1"': 3.074025253485797e-05, '"SGO2"': 3.072725069983614e-05, '"CCDC15-DT"': 3.0725680488198344e-05, '"SLC41A3"': 3.072406862239605e-05, '"FOXF2"': 3.0722545863126606e-05, '"CDHR3"': 3.072024098829139e-05, '"BCAR1"': 3.071203064422834e-05, '"HBM"': 3.070941325816115e-05, '"MT-TE"': 3.0707379440287e-05, '"IL18"': 3.070341604186487e-05, '"PSPN"': 3.070195795135311e-05, '"CPNE2"': 3.069879190388637e-05, '"MYOM3"': 3.069158737882745e-05, '"NCKIPSD"': 3.0672016113947816e-05, '"NEU1"': 3.0669677835791566e-05, '"AXIN1"': 3.066830838898171e-05, '"LRRC45"': 3.0667209870617205e-05, '"MT-TA"': 3.065413401986426e-05, '"C16orf91"': 3.064834910084419e-05, '"LINC00320"': 3.064623852706772e-05, '"TINF2"': 3.064006653268822e-05, '"ZNF865"': 3.063429611951315e-05, '"FAM210B"': 3.0634141540895695e-05, '"PTPDC1"': 3.062885498373353e-05, '"FASTKD3"': 3.0624306385393676e-05, '"KCTD2"': 3.0620912733511426e-05, '"IMMP2L"': 3.062087731203157e-05, '"SNHG6"': 3.060641201887151e-05, '"ST3GAL6"': 3.0602595340310635e-05, '"MAN1B1-DT"': 3.058552725324609e-05, '"SERINC2"': 3.0584623511882964e-05, '"RTL8C"': 3.05669865740158e-05, '"MAGEA12"': 3.055688161571648e-05, '"CDCA4"': 3.055612912671604e-05, '"MYH15"': 3.054402577985068e-05, '"CDH8"': 3.0533236889784726e-05, '"ERP27"': 3.0523455684373304e-05, '"EFNA1"': 3.051837852204393e-05, '"WIPF2"': 3.0512804164806223e-05, '"MREG"': 3.0469244996239044e-05, '"ORMDL3"': 3.0462958931576567e-05, '"TMEM184B"': 3.0451428492458804e-05, '"P2RY2"': 3.0447673713533388e-05, '"RAB3GAP1"': 3.043740751571382e-05, '"CARD9"': 3.043037824553462e-05, '"ELF4"': 3.042568377115196e-05, '"DBT"': 3.041614157816702e-05, '"CERS6"': 3.0414319701012473e-05, '"OAZ3"': 3.0402914490255458e-05, '"DLX6"': 3.038626698181253e-05, '"AAMDC"': 3.0380066868566626e-05, '"BCL7B"': 3.0374657709424237e-05, '"NAIP"': 3.0374535801984047e-05, '"UNC13D"': 3.0370718213893745e-05, '"SEC61G"': 3.0362820788153713e-05, '"STAT2"': 3.036282078815365e-05, '"PANX2"': 3.034777588310643e-05, '"TNFRSF14"': 3.0347101630367627e-05, '"CDC42BPG"': 3.0346423558574116e-05, '"MSTO1"': 3.0334499293553325e-05, '"DHRS4"': 3.031557753657079e-05, '"CHN1"': 3.0315268872363776e-05, '"PAN2"': 3.0310895239813812e-05, '"RBAK"': 3.030824273574754e-05, '"CDA"': 3.0301251581184894e-05, '"SMCR5"': 3.0290915019861004e-05, '"GLB1"': 3.0287331494416237e-05, '"GRB14"': 3.0276669900165067e-05, '"OR7E14P"': 3.0242594659712456e-05, '"MSH5"': 3.023792392822388e-05, '"TBC1D7"': 3.023335440169475e-05, '"CD2AP-DT"': 3.0231822387437875e-05, '"VPS45"': 3.0231576394806605e-05, '"DENND3-AS1"': 3.0231301449207185e-05, '"SQOR"': 3.022908094119167e-05, '"INSR"': 3.0200574772420043e-05, '"IFI6"': 3.0195693435310744e-05, '"CEP250"': 3.0188494813297706e-05, '"PAPSS2"': 3.0176922358362184e-05, '"LTBP4"': 3.017301489090976e-05, '"RUSC1"': 3.0170077331915744e-05, '"SLC29A2"': 3.016403916253011e-05, '"RNF227"': 3.0154122769603667e-05, '"PPFIA3"': 3.0150992257713675e-05, '"PARS2"': 3.0145298101111867e-05, '"LINC01854"': 3.0135781308655982e-05, '"FBF1"': 3.013264201552405e-05, '"TCEAL1"': 3.010849396299175e-05, '"TEX261"': 3.010849396299175e-05, '"UBTD1"': 3.010849396299175e-05, '"C1orf115"': 3.0107451565332827e-05, '"ABHD14A"': 3.009048007836443e-05, '"GM2A"': 3.0059665324597456e-05, '"CRIP2"': 3.004215321358177e-05, '"KDM3A"': 3.0027664161671358e-05, '"COMMD10"': 3.000227643822832e-05, '"LIPE-AS1"': 2.995047322115258e-05, '"CTDSP2"': 2.9945825651253386e-05, '"ZNF580"': 2.991933344520746e-05, '"WASF3"': 2.9903464106713924e-05, '"RPL5P3"': 2.988375754337012e-05, '"CYHR1"': 2.985936263925305e-05, '"RPL34P1"': 2.9855983420541725e-05, '"DCAF7"': 2.9837301052003357e-05, '"DNAAF5"': 2.9822832484161582e-05, '"PMEPA1"': 2.9793354657408853e-05, '"EIF3F"': 2.9686450237404224e-05, '"NRXN3"': 2.9679552002794218e-05, '"NECAB3"': 2.9593116771283973e-05, '"PSMD10P2"': 2.958177333477776e-05, '"RAD51"': 2.9576713269889783e-05, '"MIR320A"': 2.9571641359984075e-05, '"VPS16"': 2.956142442691419e-05, '"HOXB2"': 2.9545076701930468e-05, '"HMGN1P26"': 2.95060829832571e-05, '"ARNTL"': 2.9502161602617443e-05, '"KLLN"': 2.9490718443355626e-05, '"NPRL2"': 2.938270030685043e-05, '"FAM171B"': 2.9346174150286e-05, '"SLC25A22"': 2.9292237606410974e-05, '"AKT1"': 2.9241767260164447e-05, '"NTN4"': 2.9212476762843096e-05, '"LMX1B"': 2.918961527649665e-05, '"CBX6"': 2.9182441787092572e-05, '"VRK3"': 2.9151559242135767e-05, '"CRYZ"': 2.9029362191029497e-05, '"CAPN10"': 2.900599902086517e-05, '"ACADS"': 2.8979425439379555e-05, '"LINC01963"': 2.8978189132964965e-05, '"BAHD1"': 2.89183148707136e-05, '"ZNF169"': 2.8740648264778598e-05, '"PTK2B"': 2.8667815550285164e-05, '"CANT1"': 2.862780245740207e-05, '"DTX2"': 2.8616983182096933e-05, '"TNS4"': 2.849765141125053e-05, '"PLD1"': 2.848535304187762e-05, '"TCEAL3"': 2.8421333259628218e-05, '"BMP1"': 2.835472907732884e-05, '"GOLGA5"': 2.822354879096067e-05, '"NAGK"': 2.813104015305626e-05, '"AMBRA1"': 2.809442041356865e-05, '"MYO1C"': 2.7911686435495577e-05, '"UBQLN4"': 2.7852345196502554e-05, '"B3GALT1"': 2.7852345196502554e-05, '"FOXRED2"': 2.7418010348881346e-05, '"TBC1D13"': 2.7342060181709954e-05, '"CDT1"': 2.7308784111887148e-05, '"ABTB1"': 2.7264573768954354e-05, '"LAMTOR2"': 2.7133233705854513e-05, '"RAB12"': 2.7122492590938863e-05, '"ACYP2"': 2.703341100861139e-05, '"JADE1"': 2.669112315219052e-05, '"MAP2K3"': 2.6582558509995783e-05, '"HK1"': 2.6379532769580778e-05, '"MDC1"': 2.6344932217617784e-05, '"DYNLT1"': 2.628248292503885e-05, '"PPIL1"': 2.5550715525907856e-05, '"NKX2-1"': 2.5550715525907843e-05, '"LEMD3"': 2.551925616959596e-05, '"TMEM45A"': 2.5446935517690716e-05, '"KBTBD3"': 2.5342864958809203e-05, '"MAGEA3"': 2.532435145879754e-05, '"RHOV"': 2.532435145879753e-05, '"IFIT1"': 2.532435145879753e-05, '"PROSER2"': 2.532435145879753e-05, '"SYVN1"': 2.5067110676852302e-05, '"CENPM"': 2.392430265899621e-05, '"KLRK1-AS1"': 2.3856502047835057e-05, '"RBP1"': 2.3856502047835057e-05, '"IQANK1"': 2.3813619292373067e-05, '"IMPACT"': 2.3813619292373067e-05, '"PXMP4"': 2.3813619292373067e-05, '"NELFB"': 2.375893589888364e-05, '"CDK5"': 2.3732181017071506e-05, '"SAT2"': 2.3732181017071506e-05, '"LINC01559"': 2.36549227165851e-05, '"INKA1"': 2.3654234632534966e-05, '"HCFC1R1"': 2.3654234632534966e-05, '"NR2F6"': 2.3654234632534966e-05, '"NARS2"': 2.350041625954903e-05, '"DRD4"': 2.205381255436931e-05, '"ASNSD1"': 2.1292262938256545e-05, '"OPRM1"': 2.1266046807996633e-05, '"VMA21"': 2.1266046807996633e-05, '"RPS15AP29"': 2.1205779598075607e-05, '"FLAD1"': 2.11676615932205e-05, '"LRRFIP2"': 2.111905413234101e-05, '"TNIP1"': 2.1075945774094224e-05, '"KDM5C"': 2.1075945774094224e-05, '"AFAP1L2"': 2.102598634003108e-05, '"TNKS1BP1"': 2.102598634003108e-05, '"SSNA1"': 2.0889258897376915e-05, '"DYRK4"': 2.0603270260941863e-05, '"NEK6"': 1.583929059925576e-05, '"LINC00471"': 1.583929059925576e-05, '"TMEM241"': 1.5827719661748464e-05, '"SMIM1"': 1.5821454011381007e-05, '"BAIAP2-DT"': 1.581144389295854e-05, '"SFXN3"': 1.5776380844578868e-05, '"CACHD1"': 1.5771791323721084e-05, '"PIGC"': 1.573642000292702e-05, '"POLE4"': 1.5666944173032688e-05, '"ARRDC1"': 1.5652905191499856e-05, '"RNF19B"': 1.5639236349453654e-05, '"HYAL3"': 1.5587749151595388e-05, '"SYCE1L"': 1.5562498873824437e-05, '"CALB1"': 1.5334432826845063e-05, '"NAB2"': 1.0499039489681176e-05, '"PCDHGA10"': 1.0486577252060997e-05, '"MAP3K2-DT"': 1.0434925943114031e-05, '"TNFAIP8L1"': 1.0421745947425856e-05, '"ZBTB26"': 1.0172260021908524e-05, '"KIF9"': 2.8588640013366092e-06, '"CTIF"': 0.0, '"RNF123"': 0.0, '"CCDC97"': 0.0, '"RPL12P42"': 0.0, '"TRPT1"': 0.0, '"PARP12"': 0.0, '"ABTB2"': 0.0, '"REP15"': 0.0, '"NDST2"': 0.0, '"GBP2"': 0.0, '"MARCHF3"': 0.0, '"EGFLAM"': 0.0, '"ANXA6"': 0.0, '"C12orf50"': 0.0, '"RRAGD"': 0.0, '"ZSCAN18"': 0.0, '"MB"': 0.0, '"ZNRF2"': 0.0, '"UFSP1"': 0.0, '"EXOSC10-AS1"': 0.0, '"PIGCP1"': 0.0, '"SERTAD4-AS1"': 0.0, '"PXDN"': 0.0, '"AQP11"': 0.0, '"LBHD2"': 0.0, '"MS4A10"': 0.0, '"LINC01615"': 0.0, '"KLHL22"': 0.0, '"GAS7"': 0.0, '"ADAP1"': 0.0, '"RFTN1"': 0.0, '"ZNF837"': 0.0, '"MFAP3L"': 0.0, '"SERPINF1"': 0.0, '"MAP3K9-DT"': 0.0, '"LRFN4"': 0.0, '"MOSPD3"': 0.0, '"HLA-G"': 0.0, '"ECHDC3"': 0.0, '"LY6G6C"': 0.0, '"LGR6"': 0.0, '"RSPH1"': 0.0, '"JPH3"': 0.0, '"E4F1"': 0.0, '"PPIEL"': 0.0, '"ZSCAN9"': 0.0, '"TTLL1"': 0.0, '"TMEM182"': 0.0, '"IRF2-DT"': 0.0, '"MAP7D2"': 0.0, '"ARMCX6"': 0.0, '"MYPOP"': 0.0, '"RAB11B-AS1"': 0.0, '"PFKFB4"': 0.0, '"SLAMF9"': 0.0, '"BEX5"': 0.0, '"TMEM143"': 0.0, '"ZNF416"': 0.0, '"B4GALNT2"': 0.0, '"LYPD6"': 0.0, '"SNORA66"': 0.0, '"FAM166C"': 0.0, '"CNFN"': 0.0, '"TRDN-AS1"': 0.0, '"FAM43A"': 0.0, '"CCR12P"': 0.0, '"LPAR5"': 0.0, '"PLXND1"': 0.0, '"TNFRSF11B"': 0.0, '"OR3A3"': 0.0, '"TRAM1L1"': 0.0, '"ZCRB1P1"': 0.0, '"PCDHGC3"': 0.0, '"ZNF687-AS1"': 0.0, '"MT1G"': 0.0, '"SNN"': 0.0, '"PWWP2B"': 0.0, '"TUSC1"': 0.0, '"NR1D1"': 0.0, '"ARMCX5"': 0.0, '"CHMP1B2P"': 0.0, '"ABCC13"': 0.0, '"KATNB1"': 0.0, '"ST20"': 0.0, '"RPS12P16"': 0.0, '"TICAM1"': 0.0, '"DTX4"': 0.0, 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'"LRTM1"': 0.0, '"ZBED2"': 0.0, '"ERF"': 0.0, '"DYNLT2"': 0.0, '"TAGAP-AS1"': 0.0, '"GATA2-AS1"': 0.0, '"GLMP"': 0.0, '"UST"': 0.0, '"RCBTB2"': 0.0, '"RTL8A"': 0.0, '"RNF32"': 0.0, '"MIF4GD-DT"': 0.0, '"MYL9"': 0.0, '"RAB40C"': 0.0, '"ELFN2"': 0.0, '"SETMAR"': 0.0, '"PROS1"': 0.0, '"ARID5A"': 0.0, '"SMIM20"': 0.0, '"TM7SF2"': 0.0, '"EHD3"': 0.0, '"KDM6B"': 0.0, '"COL27A1"': 0.0, '"ITGB6"': 0.0, '"MAPK7"': 0.0, '"BCKDHB"': 0.0, '"LINC01816"': 0.0, '"AP1G2"': 0.0, '"TXNRD3"': 0.0, '"H2AW"': 0.0, '"SERPINB7"': 0.0, '"LTBP2"': 0.0, '"WDR90"': 0.0, '"CAPNS2"': 0.0, '"ASCL2"': 0.0, '"SAP30L"': 0.0, '"RHOXF2"': 0.0, '"KIF3C"': 0.0, '"GRK4"': 0.0, '"BICRA"': 0.0, '"CXXC5"': 0.0, '"UPRT"': 0.0, '"NPIPB4"': 0.0, '"CNEP1R1"': 0.0, '"PYCR1"': 0.0, '"EDAR"': 0.0, '"NDUFB4"': 0.0, '"PODXL2"': 0.0, '"DKK1"': 0.0, '"NOVA2"': 0.0, '"PLK4"': 0.0, '"WWOX-AS1"': 0.0, '"LINC00683"': 0.0, '"HFE"': 0.0, '"NANOS1"': 0.0, '"NECTIN4"': 0.0, '"RPL12P13"': 0.0, '"CRYM-AS1"': 0.0, '"ZKSCAN4"': 0.0, '"ADA"': 0.0, '"TNFRSF11A"': 0.0, '"C2orf27A"': 0.0, '"OBSL1"': 0.0, '"LAX1"': 0.0, '"CATSPERB"': 0.0, '"SETBP1"': 0.0, '"GJB3"': 0.0, '"ATP8B2"': 0.0, '"ZNF385A"': 0.0, '"RPL9P32"': 0.0, '"FSD1L"': 0.0, '"CNKSR1"': 0.0, '"VAMP2"': 0.0, '"FAM241B"': 0.0, '"LINC01102"': 0.0, '"LINC01266"': 0.0, '"SOX21-AS1"': 0.0, '"LPP-AS2"': 0.0, '"CHTF18"': 0.0, '"PANK1"': 0.0, '"FA2H"': 0.0, '"NSA2P4"': 0.0, '"ANXA4"': 0.0, '"SUMF1"': 0.0, '"SPRY1"': 0.0, '"STK36"': 0.0, '"TNC"': 0.0, '"LINC01637"': 0.0, '"LASTR"': 0.0, '"RASSF3"': 0.0, '"KBTBD4"': 0.0, '"RIMKLA"': 0.0, '"RAB42"': 0.0, '"ARHGEF17"': 0.0, '"KLHDC3"': 0.0, '"RAB30"': 0.0, '"MLH3"': 0.0, '"ITGBL1"': 0.0, '"EVI5L"': 0.0, '"PPP1R3G"': 0.0, '"REEP1"': 0.0, '"ABHD17A"': 0.0, '"GSDME"': 0.0, '"NXT2"': 0.0, '"RBM43"': 0.0, '"BLCAP"': 0.0, '"YWHAQP5"': 0.0, '"LINC01322"': 0.0, '"CCPG1"': 0.0, '"JAZF1"': 0.0, '"FZD1"': 0.0, '"ZNF577"': 0.0, '"TEDC2"': 0.0, '"LINC00663"': 0.0, '"C1orf53"': 0.0, '"MYH7B"': 0.0, '"CKB"': 0.0, '"NTRK2"': 0.0, '"BDKRB2"': 0.0, '"SSPN"': 0.0, '"RELB"': 0.0, '"BMP8B"': 0.0, '"KHNYN"': 0.0, '"MAP3K6"': 0.0, '"ZNF45"': 0.0, '"ATP5PDP3"': 0.0, '"CADM1"': 0.0, '"LINC01415"': 0.0, '"ST3GAL1-DT"': 0.0, '"TAB1"': 0.0, '"IL1A"': 0.0, '"SMARCAL1"': 0.0, '"EPOP"': 0.0, '"LINC00960"': 0.0, '"MAU2"': 0.0, '"DYNC1LI2-DT"': 0.0, '"LOXL2"': 0.0, '"PWRN1"': 0.0, '"IFT74"': 0.0, '"LRRC61"': 0.0, '"SLC6A9"': 0.0, '"GBA"': 0.0, '"TNFSF13B"': 0.0, '"ZNF433"': 0.0, '"MBTPS1-DT"': 0.0, '"ACTBP2"': 0.0, '"SH2B3"': 0.0, '"NOD1"': 0.0, '"CA11"': 0.0, '"NARF-AS2"': 0.0, '"DOHH"': 0.0, '"UBALD2"': 0.0, '"ROBO3"': 0.0, '"DPPA4"': 0.0, '"ZNF417"': 0.0, '"COL9A2"': 0.0, '"FOXO3B"': 0.0, '"NDUFA8"': 0.0, '"MORN3"': 0.0, '"MRTFA"': 0.0, '"NRF1"': 0.0, '"MIOS-DT"': 0.0, '"BICC1"': 0.0, '"QPCTL"': 0.0, '"DNAJC3-DT"': 0.0, '"ZBED8"': 0.0, '"SUN2"': 0.0, '"MYO1F"': 0.0, '"MED11"': 0.0, '"TRNP1"': 0.0, '"DENND4A"': 0.0, '"ANO7"': 0.0, '"NLRP2B"': 0.0, '"GOLGA2P5"': 0.0, '"ARID4A"': 0.0, '"SIGLEC10"': 0.0, '"CUTC"': 0.0, '"LTB4R"': 0.0, '"DLG4"': 0.0, '"RNF185"': 0.0, '"TEF"': 0.0, '"B4GAT1"': 0.0, '"ZNF418"': 0.0, '"ZCWPW1"': 0.0, '"FAM111A-DT"': 0.0, '"YTHDF3"': 0.0, '"FBLN2"': 0.0, '"CHMP1A"': 0.0, '"SMPDL3A"': 0.0, '"MRPL10"': 0.0, '"HOXB3"': 0.0, '"HMGN1P17"': 0.0, '"NEU3"': 0.0, '"RNF166"': 0.0, '"SFTA1P"': 0.0, '"FGFBP3"': 0.0, '"PARP16"': 0.0, '"FAM114A1"': 0.0, '"VAT1"': 0.0, '"TROAP"': 0.0, '"NAALADL2"': 0.0, '"PLIN3"': 0.0, '"MICB"': 0.0, '"TUBB6"': 0.0, '"NRG4"': 0.0, '"AQP3"': 0.0, '"KDM4C"': 0.0, '"TRPM2"': 0.0, '"EZH1"': 0.0, '"USP32"': 0.0, '"ZNF558"': 0.0, '"COX4I2"': 0.0, '"TRAPPC6A"': 0.0, '"RAB5B"': 0.0, '"SMC1B"': 0.0, '"WDR27"': 0.0, '"EGLN2"': 0.0, '"PHACTR1"': 0.0, '"TF"': 0.0, '"MXD3"': 0.0, '"FBXO30"': 0.0, '"RFK"': 0.0, '"OCEL1"': 0.0, '"MOGS"': 0.0, '"SULT2A1"': 0.0, '"LINC01087"': 0.0, '"PRKCD"': 0.0, '"KHDC1"': 0.0, '"LINC02245"': 0.0, '"OGFRL1"': 0.0, '"FKTN"': 0.0, '"FBXO2"': 0.0, '"CNDP1"': 0.0, '"CLCF1"': 0.0, '"SPP1"': 0.0, '"TK2"': 0.0, '"ZNF182"': 0.0, '"ADGRE1"': 0.0, '"ANKEF1"': 0.0, '"KIFC3"': 0.0, '"DUSP5"': 0.0, '"ZNF335"': 0.0, '"EML1"': 0.0, '"LCAT"': 0.0, '"ARL10"': 0.0, '"DELE1"': 0.0, '"ZBTB34"': 0.0, '"PITPNC1"': 0.0, '"MAD2L2"': 0.0, '"MSX1"': 0.0, '"ESYT3"': 0.0, '"C19orf47"': 0.0, '"P3H1"': 0.0, '"MYO5C"': 0.0, '"RCCD1-AS1"': 0.0, '"LINC02029"': 0.0, '"TMEM39B"': 0.0, '"CCL26"': 0.0, '"APEH"': 0.0, '"HMGB1P8"': 0.0, '"NIBAN2"': 0.0, '"ZNF22"': 0.0, '"PHF1"': 0.0, '"ZNF777"': 0.0, '"PECAM1"': 0.0, '"PDE1B"': 0.0, '"ARL2"': 0.0, '"OSBPL3"': 0.0, '"CHPF"': 0.0, '"IL10RB"': 0.0, '"LINC01460"': 0.0, '"RBSN"': 0.0, '"NLRC5"': 0.0, '"ZNF516"': 0.0, '"ADGRF4"': 0.0, '"TATDN2"': 0.0, '"MFSD5"': 0.0, '"ODAD2"': 0.0, '"ZG16B"': 0.0, '"MSRB3"': 0.0, '"CDK9"': 0.0, '"CENPBD1"': 0.0, '"DOC2A"': 0.0, '"NLRX1"': 0.0, '"TCF15"': 0.0, '"ALDOC"': 0.0, '"ATF3"': 0.0, '"CDH24"': 0.0, '"CDPF1"': 0.0, '"MBD1"': 0.0, '"LINC02672"': 0.0, '"MT-TH"': 0.0, '"B4GALT2"': 0.0, '"IL12B"': 0.0, '"GNG4"': 0.0, '"NEBL"': 0.0, '"SLC8A1"': 0.0, '"BMPR2"': 0.0, '"TSHZ2"': 0.0, '"ABHD12B"': 0.0, '"WWTR1-AS1"': 0.0, '"ACVR1"': 0.0, '"APLF"': 0.0, '"BAMBI"': 0.0, '"SUSD5"': 0.0, '"ZNF826P"': 0.0, '"PDE9A"': 0.0, '"FAM214B"': 0.0, '"MEX3D"': 0.0, '"ZNF784"': 0.0, '"CHMP7"': 0.0, '"TSNARE1"': 0.0, '"RRAGA"': 0.0, '"AKAP5"': 0.0, '"ADNP-AS1"': 0.0, '"GRIN2D"': 0.0, '"NEUROD1"': 0.0, '"MAGEA4"': 0.0, '"DHX35-DT"': 0.0, '"KCNMB4"': 0.0, '"S100A4"': 0.0, '"PTCH1"': 0.0, '"MARVELD1"': 0.0, '"TGDS"': 0.0, '"GREP1"': 0.0, '"CCDC191"': 0.0, '"CTU2"': 0.0, '"HMBOX1"': 0.0, '"RHBDL2"': 0.0, '"PKN1"': 0.0, '"NEUROD2"': 0.0, '"CAVIN2"': 0.0, '"FKBP9P1"': 0.0, '"VPS26B"': 0.0, '"MAGI2-AS3"': 0.0, '"ADORA2B"': 0.0, '"FRAT2"': 0.0, '"FHDC1"': 0.0, '"SLC35B3"': 0.0, '"RNASEH1-AS1"': 0.0, '"LINC00911"': 0.0, '"ATP6V1B2"': 0.0, '"MIR663B"': 0.0, '"HOXA11-AS"': 0.0, '"S1PR3"': 0.0, '"CAPNS1"': 0.0, '"FAM13B"': 0.0, '"ZYG11A"': 0.0, '"YBEY"': 0.0, '"ING2"': 0.0, '"C17orf99"': 0.0, '"OXNAD1"': 0.0, '"PEX11A"': 0.0, '"ARHGEF28"': 0.0, '"PIK3R2"': 0.0, '"DPRX"': 0.0, '"SDSL"': 0.0, '"RN7SL471P"': 0.0, '"IFNGR2"': 0.0, '"TMEM44-AS1"': 0.0, '"ESR1"': 0.0, '"HHLA2"': 0.0, '"DNAAF9"': 0.0, '"FUT11"': 0.0, '"SIX2"': 0.0, '"HBA1"': 0.0, '"HECA"': 0.0, '"CYP2C9"': 0.0, '"LERFS"': 0.0, '"FHL3"': 0.0, '"TMEM25"': 0.0, '"SNHG18"': 0.0, '"CMAS"': 0.0, '"RNF25"': 0.0, '"RIPK1"': 0.0, '"AKAP6"': 0.0, '"NLRP8"': 0.0, '"TNK2"': 0.0, '"CLEC4OP"': 0.0, '"SLC2A3"': 0.0, '"NRXN2"': 0.0, '"ABCA7"': 0.0, '"C11orf49"': 0.0, '"ARAP1"': 0.0, '"PYCARD"': 0.0, '"DERA"': 0.0, '"EEF1A1P25"': 0.0, '"ZNF90P3"': 0.0, '"PPP1R14C"': 0.0, '"CLHC1"': 0.0, '"GPRC5C"': 0.0, '"AMFR"': 0.0, '"BACE2"': 0.0, '"TRIM7"': 0.0, '"MTFP1"': 0.0, '"SF3B4"': 0.0, '"ALX1"': 0.0, '"NUP62CL"': 0.0, '"NOC2LP1"': 0.0, '"TJAP1"': 0.0, '"C11orf98"': 0.0, '"VASH2"': 0.0, '"TBCCD1"': 0.0, '"LINC02894"': 0.0, '"RNLS"': 0.0, '"OCRL"': 0.0, '"HIP1R"': 0.0, '"MAP3K12"': 0.0, '"LARGE1"': 0.0, '"GYS1"': 0.0, '"ADPRM"': 0.0, '"CLMN"': 0.0, '"DUSP12"': 0.0, '"SLC31A2"': 0.0, '"KCNJ15"': 0.0, '"CCDC153"': 0.0, '"FTHL17"': 0.0, '"PPP2R5D"': 0.0, '"WDR35"': 0.0, '"RELA"': 0.0, '"IRS1"': 0.0, '"VAMP7"': 0.0, '"ZBTB46"': 0.0, '"TMPOP2"': 0.0, '"PRDM11"': 0.0, '"LINC02178"': 0.0, '"ZNF571-AS1"': 0.0, '"FOXO3"': 0.0, '"CCNY"': 0.0, '"CKS1B"': 0.0, '"SLC25A12"': 0.0, '"LINC-PINT"': 0.0, '"DLGAP1-AS2"': 0.0, '"SLC30A10"': 0.0, '"CLDN15"': 0.0, '"TLX3"': 0.0, '"SEPTIN1"': 0.0, '"C5orf38"': 0.0, '"FSIP1"': 0.0, '"PER3"': 0.0, '"NKX2-8"': 0.0, '"HLA-F"': 0.0, '"SERGEF"': 0.0, '"PGPEP1"': 0.0, '"PPP2R5B"': 0.0, '"RHBDD2"': 0.0, '"SNX22"': 0.0, '"MCM5"': 0.0, '"ESRP2"': 0.0, '"CD151"': 0.0, '"CTTN-DT"': 0.0, '"SLC2A6"': 0.0, '"SELENON"': 0.0, '"FAM114A2"': 0.0, '"LINC01116"': 0.0, '"FAM169A"': 0.0, '"ISOC2"': 0.0, '"EEPD1"': 0.0, '"BRWD3"': 0.0, '"LINC01091"': 0.0, '"B3GLCT"': 0.0, '"MAGED2"': 0.0, '"TNFRSF10B"': 0.0, '"WDR6"': 0.0, '"TRAPPC14"': 0.0, '"PANX1"': 0.0, '"CASP3"': 0.0, '"PFKFB2"': 0.0, '"PIM1"': 0.0, '"ESRRA"': 0.0, '"TBC1D25"': 0.0, '"SAP30L-AS1"': 0.0, '"PALM"': 0.0, '"LRP4"': 0.0, '"UNC119B"': 0.0, '"ARMCX4"': 0.0, '"EIPR1"': 0.0, '"CA9"': 0.0, '"CABP4"': 0.0, '"MEX3C"': 0.0, '"ZBTB18"': 0.0, '"CNTROB"': 0.0, '"HECW2"': 0.0, '"AGAP1"': 0.0, '"DGLUCY"': 0.0, '"GIHCG"': 0.0, '"PKN3"': 0.0, '"PIGBOS1"': 0.0, '"SMTN"': 0.0, '"PLCD1"': 0.0, '"AFAP1L1"': 0.0, '"TTYH3"': 0.0, '"INTS14"': 0.0, '"R3HCC1L"': 0.0, '"IGSF6"': 0.0, '"RDH14"': 0.0, '"DGKD"': 0.0, '"ACSF2"': 0.0, '"AMZ1"': 0.0, '"PIGK"': 0.0, '"LONRF1"': 0.0, '"NUDT18"': 0.0, '"TLL1"': 0.0, '"SYT15"': 0.0, '"AAAS"': 0.0, '"FABP3"': 0.0, '"SLC4A1"': 0.0, '"MTLN"': 0.0, '"LDB1"': 0.0, '"SAMMSON"': 0.0, '"TMTC2"': 0.0, '"LINC01607"': 0.0, '"SENP3"': 0.0, '"GRK2"': 0.0, '"ZNF782"': 0.0, '"SYNM"': 0.0, '"FCRL5"': 0.0, '"CACNB1"': 0.0, '"DNAH11"': 0.0, '"TIMM29"': 0.0, '"PLEKHG4B"': 0.0, '"PI4K2B"': 0.0, '"HERC6"': 0.0, '"ZNF517"': 0.0, '"NECAP1"': 0.0, '"SLC25A5"': 0.0, '"HPRT1"': 0.0, '"ZBTB12"': 0.0, '"BICDL2"': 0.0, '"FSBP"': 0.0, '"RIN2"': 0.0, '"TESMIN"': 0.0, '"CCDC102A"': 0.0, '"MTUS2"': 0.0, '"CLASRP"': 0.0, '"UBXN6"': 0.0, '"SHANK2"': 0.0, '"SYTL4"': 0.0, '"MYADM"': 0.0, '"DMRTA2"': 0.0, '"FNDC10"': 0.0, '"FLACC1"': 0.0, '"SP2"': 0.0, '"RPGRIP1L"': 0.0, '"PCDHB1"': 0.0, '"FBXL15"': 0.0, '"MEX3A"': 0.0, '"ART3"': 0.0, '"B4GALT7"': 0.0, '"TTL"': 0.0, '"EPHX2"': 0.0, '"LRRC8B"': 0.0, '"NOA1"': 0.0, '"WT1-AS"': 0.0, '"C2orf68"': 0.0, '"RAB8B"': 0.0, '"PPFIA4"': 0.0, '"COA5"': 0.0, '"RELN"': 0.0, '"OR2A5"': 0.0, '"RTN4R"': 0.0, '"LDLRAP1"': 0.0, '"SCAPER"': 0.0, '"FUT2"': 0.0, '"THBS1-IT1"': 0.0, '"ZNF319"': 0.0, '"DMPK"': 0.0, '"LINC01551"': 0.0, '"GALNS"': 0.0, '"PSMG3-AS1"': 0.0, '"SLC9A8"': 0.0, '"ADO"': 0.0, '"MIB2"': 0.0, '"CCDC61"': 0.0, '"NSMCE3"': 0.0, '"C6orf136"': 0.0, '"RASGEF1B"': 0.0, '"MFSD13A"': 0.0, '"HK2"': 0.0, '"DTD2"': 0.0, '"SLC35A2"': 0.0, '"EFCAB2"': 0.0, '"PLAAT4"': 0.0, '"TRIM39"': 0.0, '"THSD7A"': 0.0, '"AMOTL2"': 0.0, '"CCNG1"': 0.0, '"MORN2"': 0.0, '"NEDD1"': 0.0, '"CHTOP"': 0.0, '"COL19A1"': 0.0, '"TSPAN15"': 0.0, '"RRM1"': 0.0, '"DPYSL3"': 0.0, '"UNK"': 0.0, '"GOLGA6L2"': 0.0, '"ANXA3"': 0.0, '"ALDH5A1"': 0.0, '"GNGT1"': 0.0, '"POMK"': 0.0, '"FBXL3"': 0.0, '"TMEM144"': 0.0, '"TRMT1L"': 0.0, '"B3GALT6"': 0.0, '"RSAD1"': 0.0, '"CCDC26"': 0.0, '"CAMK2B"': 0.0, '"MSL3P1"': 0.0, '"TRPV4"': 0.0, '"IBA57"': 0.0, '"TFIP11"': 0.0, '"NFKBIE"': 0.0, '"ZNF511"': 0.0, '"IFFO2"': 0.0, '"RAPGEF6"': 0.0, '"ACTR1B"': 0.0, '"MICAL2"': 0.0, '"SNURF"': 0.0, '"SCNM1"': 0.0, '"RPL23AP7"': 0.0, '"MMP28"': 0.0, '"POLA2"': 0.0, '"LINC01560"': 0.0, '"TYMP"': 0.0, '"AVPI1"': 0.0, '"RNASET2"': 0.0, '"MAP1LC3B2"': 0.0, '"TGM2"': 0.0, '"NUMBL"': 0.0, '"TYMSOS"': 0.0, '"GMIP"': 0.0, '"C12orf57"': 0.0, '"PRRG2"': 0.0, '"DOCK8-AS1"': 0.0, '"ATP1B2"': 0.0, '"GPRIN2"': 0.0, '"ANKRD27"': 0.0, '"MRPL49"': 0.0, '"KCTD14"': 0.0, '"MCM3AP-AS1"': 0.0, '"ABHD10"': 0.0, '"TXNDC15"': 0.0, '"FKBP9"': 0.0, '"SPG21"': 0.0, '"CCDC74A"': 0.0, '"PPM1A"': 0.0, '"PAQR9-AS1"': 0.0, '"ANO8"': 0.0, '"CARD16"': 0.0, '"GNPAT"': 0.0, '"EMP2"': 0.0, '"POTEF"': 0.0, '"PID1"': 0.0, '"SMO"': 0.0, '"OSTF1"': 0.0, '"UVSSA"': 0.0, '"RAP1GAP2"': 0.0, '"COMT"': 0.0, '"TMEM125"': 0.0, '"THEM4"': 0.0, '"FYCO1"': 0.0, '"USP30"': 0.0, '"ZNF256"': 0.0, '"ARHGEF35"': 0.0, '"POLG"': 0.0, '"VGLL1"': 0.0, '"HAUS5"': 0.0, '"ZNF542P"': 0.0, '"MINK1"': 0.0, '"SMG8"': 0.0, '"CASC9"': 0.0, '"DENND4B"': 0.0, '"HAS3"': 0.0, '"TEX30"': 0.0, '"SELENOH"': 0.0, '"TOR2A"': 0.0, '"TRAF2"': 0.0, '"SLC24A2"': 0.0, '"OR4K17"': 0.0, '"SHISA5"': 0.0, '"PLCE1"': 0.0, '"MTO1"': 0.0, '"ORC4"': 0.0, '"TBL1X"': 0.0, '"ZNF202"': 0.0, '"PADI2"': 0.0, '"RPS6KL1"': 0.0, '"TWIST1"': 0.0, '"FOXO4"': 0.0, '"DHX40"': 0.0, '"NEIL3"': 0.0, '"POTEM"': 0.0, '"ARL13B"': 0.0, '"TAFAZZIN"': 0.0, '"LINC01546"': 0.0, '"GMEB2"': 0.0, '"NMRK1"': 0.0, '"NCK1-DT"': 0.0, '"SLC39A11"': 0.0, '"FABP6"': 0.0, '"RECQL5"': 0.0, '"ZNF850"': 0.0, '"MIR194-2HG"': 0.0, '"ANKRD40"': 0.0, '"CFAP45"': 0.0, '"ITSN2"': 0.0, '"DIPK1A"': 0.0, '"HPCA"': 0.0, '"MAPK8IP3"': 0.0, '"VPS51"': 0.0, '"TAF6L"': 0.0, '"MAN1C1"': 0.0, '"LINC02210"': 0.0, '"ADCK1"': 0.0, '"SIX3"': 0.0, '"NCAM2"': 0.0, '"TMEM8B"': 0.0, '"DYSF"': 0.0, '"APOL3"': 0.0, '"LINC02080"': 0.0, '"LYPD4"': 0.0, '"NOMO3"': 0.0, '"CPB1"': 0.0, '"ZNF688"': 0.0, '"SAMHD1"': 0.0, '"GSEC"': 0.0, '"CYP2J2"': 0.0, '"PBLD"': 0.0, '"H3C12"': 0.0, '"SIRT1"': 0.0, '"ANKRD44"': 0.0, '"LINC02345"': 0.0, '"HHAT"': 0.0, '"OVOL2"': 0.0, '"ZC3H4"': 0.0, '"LINC00342"': 0.0, '"KRBOX4"': 0.0, '"PGBD1"': 0.0, '"NAA40"': 0.0, '"TSGA10"': 0.0, '"STC2"': 0.0, '"DDIT3"': 0.0, '"ZFAS1"': 0.0, '"BATF3"': 0.0, '"PMPCA"': 0.0, '"SCCPDH"': 0.0, '"ZNF682"': 0.0}

Apparently, the gene that is more important in determining wether a cell is under hypoxic or normoxic condition is still the NDRG1, which wasn't in the first genes in the other analysis.

In [ ]:
# to see the less important ones.
print({k: v for k, v in sorted(genes.items(), key=lambda item: item[1], reverse=False)})
{'"CTIF"': 0.0, '"RNF123"': 0.0, '"CCDC97"': 0.0, '"RPL12P42"': 0.0, '"TRPT1"': 0.0, '"PARP12"': 0.0, '"ABTB2"': 0.0, '"REP15"': 0.0, '"NDST2"': 0.0, '"GBP2"': 0.0, '"MARCHF3"': 0.0, '"EGFLAM"': 0.0, '"ANXA6"': 0.0, '"C12orf50"': 0.0, '"RRAGD"': 0.0, '"ZSCAN18"': 0.0, '"MB"': 0.0, '"ZNRF2"': 0.0, '"UFSP1"': 0.0, '"EXOSC10-AS1"': 0.0, '"PIGCP1"': 0.0, '"SERTAD4-AS1"': 0.0, '"PXDN"': 0.0, '"AQP11"': 0.0, '"LBHD2"': 0.0, '"MS4A10"': 0.0, '"LINC01615"': 0.0, '"KLHL22"': 0.0, '"GAS7"': 0.0, '"ADAP1"': 0.0, '"RFTN1"': 0.0, '"ZNF837"': 0.0, '"MFAP3L"': 0.0, '"SERPINF1"': 0.0, '"MAP3K9-DT"': 0.0, '"LRFN4"': 0.0, '"MOSPD3"': 0.0, '"HLA-G"': 0.0, '"ECHDC3"': 0.0, '"LY6G6C"': 0.0, '"LGR6"': 0.0, '"RSPH1"': 0.0, '"JPH3"': 0.0, '"E4F1"': 0.0, '"PPIEL"': 0.0, '"ZSCAN9"': 0.0, '"TTLL1"': 0.0, '"TMEM182"': 0.0, '"IRF2-DT"': 0.0, '"MAP7D2"': 0.0, '"ARMCX6"': 0.0, '"MYPOP"': 0.0, '"RAB11B-AS1"': 0.0, '"PFKFB4"': 0.0, '"SLAMF9"': 0.0, '"BEX5"': 0.0, '"TMEM143"': 0.0, '"ZNF416"': 0.0, '"B4GALNT2"': 0.0, '"LYPD6"': 0.0, '"SNORA66"': 0.0, '"FAM166C"': 0.0, '"CNFN"': 0.0, '"TRDN-AS1"': 0.0, '"FAM43A"': 0.0, '"CCR12P"': 0.0, '"LPAR5"': 0.0, '"PLXND1"': 0.0, '"TNFRSF11B"': 0.0, '"OR3A3"': 0.0, '"TRAM1L1"': 0.0, '"ZCRB1P1"': 0.0, '"PCDHGC3"': 0.0, '"ZNF687-AS1"': 0.0, '"MT1G"': 0.0, '"SNN"': 0.0, '"PWWP2B"': 0.0, '"TUSC1"': 0.0, '"NR1D1"': 0.0, '"ARMCX5"': 0.0, '"CHMP1B2P"': 0.0, '"ABCC13"': 0.0, '"KATNB1"': 0.0, '"ST20"': 0.0, '"RPS12P16"': 0.0, '"TICAM1"': 0.0, '"DTX4"': 0.0, '"ACBD4"': 0.0, '"S100P"': 0.0, '"FAM110C"': 0.0, '"SPN"': 0.0, '"ZNF263"': 0.0, '"NFKBID"': 0.0, '"SLC27A1"': 0.0, '"MT-TD"': 0.0, '"PLA2G6"': 0.0, '"HS1BP3"': 0.0, '"LINC01764"': 0.0, '"LBX2"': 0.0, '"AGAP1-IT1"': 0.0, '"COPZ2"': 0.0, '"MT-TC"': 0.0, '"FTH1P16"': 0.0, '"FOXE1"': 0.0, '"NUDT16L2P"': 0.0, '"UNC13C"': 0.0, '"ITGA4"': 0.0, '"DNAH7"': 0.0, '"DLX2"': 0.0, '"MTMR11"': 0.0, '"TXNDC11"': 0.0, '"ANG"': 0.0, '"ZNF212"': 0.0, '"SAMD10"': 0.0, '"BMP8A"': 0.0, '"NDOR1"': 0.0, '"DGCR6"': 0.0, '"TMEM94"': 0.0, '"ROBO1"': 0.0, '"RCCD1"': 0.0, '"SPART-AS1"': 0.0, '"TIGD5"': 0.0, '"SNX33"': 0.0, '"HOXC8"': 0.0, '"TRIM45"': 0.0, '"PGLS-DT"': 0.0, '"ROGDI"': 0.0, '"ZNF875"': 0.0, '"ITGA11"': 0.0, '"PLEKHA8P1"': 0.0, '"MT-TN"': 0.0, '"MT-TF"': 0.0, '"FBXO43"': 0.0, '"ARTN"': 0.0, '"SHF"': 0.0, '"SLC38A4"': 0.0, '"C3orf35"': 0.0, '"PLEKHG6"': 0.0, '"CACNB2"': 0.0, '"DISP1"': 0.0, '"HELQ"': 0.0, '"GPR160"': 0.0, '"FAM234B"': 0.0, '"ZFYVE1"': 0.0, '"LINC01533"': 0.0, '"ZBTB22"': 0.0, '"MT-TK"': 0.0, '"FAM131A"': 0.0, '"LRRC2"': 0.0, '"KLHL6"': 0.0, '"MT1A"': 0.0, '"LRATD1"': 0.0, '"LINC02609"': 0.0, '"SPATA2L"': 0.0, '"POLM"': 0.0, '"BBS12"': 0.0, '"NTRK3"': 0.0, '"C12orf76"': 0.0, '"SSH3"': 0.0, '"PPCDC"': 0.0, '"IPPK"': 0.0, '"NGEF"': 0.0, '"TRIM21"': 0.0, '"FNBP1P1"': 0.0, '"ADM2"': 0.0, '"BMP2"': 0.0, '"HSPD1P11"': 0.0, '"DAPK3"': 0.0, '"DXO"': 0.0, '"LY6G5C"': 0.0, '"HAP1"': 0.0, '"SPX"': 0.0, '"MPG"': 0.0, '"TRMT2A"': 0.0, '"USP35"': 0.0, '"MT-TI"': 0.0, '"TMEM128"': 0.0, '"UCK1"': 0.0, '"KRT15"': 0.0, '"PHC1"': 0.0, '"CBLL1-AS1"': 0.0, '"FGD1"': 0.0, '"RINL"': 0.0, '"CNR2"': 0.0, '"HOXA-AS2"': 0.0, '"POLR2J3"': 0.0, '"MAP4K1"': 0.0, '"ZNF804A"': 0.0, '"MUL1"': 0.0, '"PLCD3"': 0.0, '"KLC3"': 0.0, '"HDAC5"': 0.0, '"H1-6"': 0.0, '"SYDE1"': 0.0, '"FAT4"': 0.0, '"R3HCC1"': 0.0, '"SIAH1"': 0.0, '"CRY2"': 0.0, '"LINC02076"': 0.0, '"DIXDC1"': 0.0, '"STARD7-AS1"': 0.0, '"SIMC1"': 0.0, '"NTF4"': 0.0, '"ZNF747"': 0.0, '"CTBS"': 0.0, '"ARL14"': 0.0, '"NOP14-AS1"': 0.0, '"REPS2"': 0.0, '"FBXO4"': 0.0, '"PRR36"': 0.0, '"KCP"': 0.0, '"MTATP6P1"': 0.0, '"ULBP1"': 0.0, '"MEF2D"': 0.0, '"AXIN2"': 0.0, '"PKMYT1"': 0.0, '"ZNF836"': 0.0, '"SPRR3"': 0.0, '"MAP3K8"': 0.0, '"GLB1L"': 0.0, '"MIATNB"': 0.0, '"GLI4"': 0.0, '"PHC2"': 0.0, '"IL21R"': 0.0, '"PSKH1"': 0.0, '"HSPD1P5"': 0.0, '"USF1"': 0.0, '"KAT14"': 0.0, '"KSR1"': 0.0, '"CALCOCO1"': 0.0, '"KCNMA1"': 0.0, '"NUP153-AS1"': 0.0, '"SUNO1"': 0.0, '"UNC5B-AS1"': 0.0, '"CTDP1"': 0.0, '"CHST14"': 0.0, '"DAB2IP"': 0.0, '"ANKMY1"': 0.0, '"NRSN1"': 0.0, '"GPRC5D"': 0.0, '"EPB41L4A-AS1"': 0.0, '"OSCP1"': 0.0, '"THAP4"': 0.0, '"HOXA7"': 0.0, '"PARD6A"': 0.0, '"GASAL1"': 0.0, '"PROC"': 0.0, '"CLDN4"': 0.0, '"TMEM158"': 0.0, '"C17orf100"': 0.0, '"CCSER1"': 0.0, '"NLRP10"': 0.0, '"NR2F2-AS1"': 0.0, '"DTNB"': 0.0, '"GABRE"': 0.0, '"FAM193B"': 0.0, '"EAF2"': 0.0, '"IL15RA"': 0.0, '"MYO18B"': 0.0, '"ZNF395"': 0.0, '"FER1L4"': 0.0, '"HPS6"': 0.0, '"PRORSD1P"': 0.0, '"TUBBP5"': 0.0, '"WFDC3"': 0.0, '"MPRIP-AS1"': 0.0, '"STARD13-AS"': 0.0, '"PIM2"': 0.0, '"ASB2"': 0.0, '"IER5L"': 0.0, '"BMI1"': 0.0, '"COL1A1"': 0.0, '"MUS81"': 0.0, '"YWHAEP5"': 0.0, '"KIAA2012"': 0.0, '"GVINP1"': 0.0, '"FBXL16"': 0.0, '"DUT-AS1"': 0.0, '"SERPINB10"': 0.0, '"MAILR"': 0.0, '"APBA2"': 0.0, '"PIM3"': 0.0, '"LINC01695"': 0.0, '"SCN7A"': 0.0, '"CDX2"': 0.0, '"CLDND2"': 0.0, '"SH3GL3"': 0.0, '"TLR2"': 0.0, '"ATL1"': 0.0, '"PKHD1L1"': 0.0, '"DSCR8"': 0.0, '"TP73-AS1"': 0.0, '"MED26"': 0.0, '"HSD11B2"': 0.0, '"CDK6-AS1"': 0.0, '"TEP1"': 0.0, '"NDN"': 0.0, '"KIF27"': 0.0, '"H2AC16"': 0.0, '"CREB3L1"': 0.0, '"SCRN2"': 0.0, '"RUNX2"': 0.0, '"CRYBB2"': 0.0, '"ELOVL7"': 0.0, '"LOX"': 0.0, '"KAT2B"': 0.0, '"MED23"': 0.0, '"NINL"': 0.0, '"SAMD15"': 0.0, '"PORCN"': 0.0, '"PYGO1"': 0.0, '"MAD1L1"': 0.0, '"PLD2"': 0.0, '"C21orf62-AS1"': 0.0, '"LINC02615"': 0.0, '"OR5M2P"': 0.0, '"TP53INP2"': 0.0, '"DUOX1"': 0.0, '"SLC30A2"': 0.0, '"CAB39L"': 0.0, '"CABLES1"': 0.0, '"DUSP1"': 0.0, '"VPS52"': 0.0, '"KIF21B"': 0.0, '"LINC02899"': 0.0, '"RPL24P9"': 0.0, '"YPEL3"': 0.0, '"LRRC26"': 0.0, '"SLC22A5"': 0.0, '"STAG3L5P-PVRIG2P-PILRB"': 0.0, '"KMT2E-AS1"': 0.0, '"ZNF251"': 0.0, '"KRT3"': 0.0, '"RHOQP3"': 0.0, '"LRCH4"': 0.0, '"ABO"': 0.0, '"FGFR3"': 0.0, '"LENG9"': 0.0, '"IRAK3"': 0.0, '"LRFN1"': 0.0, '"NEURL1"': 0.0, '"EXOC3-AS1"': 0.0, '"FGF22"': 0.0, '"GRAMD1B"': 0.0, '"IER5"': 0.0, '"RAB15"': 0.0, '"SLC1A2"': 0.0, '"RADIL"': 0.0, '"POTEC"': 0.0, '"ALDH6A1"': 0.0, '"DENND2D"': 0.0, '"LCTL"': 0.0, '"YPEL5"': 0.0, '"IMP3"': 0.0, '"MIR137HG"': 0.0, '"INTS6-AS1"': 0.0, '"OR52A1"': 0.0, '"PEX11B"': 0.0, '"SMIM30"': 0.0, '"UPF3AP2"': 0.0, '"CNOT6LP1"': 0.0, '"SREBF2-AS1"': 0.0, '"FGD2"': 0.0, '"RASGRP2"': 0.0, '"INCA1"': 0.0, '"INTS9"': 0.0, '"BTG2"': 0.0, '"CMYA5"': 0.0, '"BCAS3"': 0.0, '"ZP3"': 0.0, '"C11orf71"': 0.0, '"LINC01667"': 0.0, '"STON1"': 0.0, '"NEK10"': 0.0, '"ZDHHC1"': 0.0, '"RASGEF1A"': 0.0, '"CRB3"': 0.0, '"FASTK"': 0.0, '"C9orf64"': 0.0, '"LINC01843"': 0.0, '"LIMD2"': 0.0, '"FIBCD1"': 0.0, '"OPTN"': 0.0, '"SPHK2"': 0.0, '"MYOSLID"': 0.0, '"RPS18P9"': 0.0, '"CSAG3"': 0.0, '"HOXC6"': 0.0, '"MSI1"': 0.0, '"TBC1D22A-DT"': 0.0, '"FAM131C"': 0.0, '"ZFYVE28"': 0.0, '"ANKRD9"': 0.0, '"AP2A1"': 0.0, '"ZNF568"': 0.0, '"C5AR1"': 0.0, '"NES"': 0.0, '"ATP6V0C"': 0.0, '"D2HGDH"': 0.0, '"PCYOX1L"': 0.0, '"MMP25-AS1"': 0.0, '"HSF2BP"': 0.0, '"ARL15"': 0.0, '"SLC9B1"': 0.0, '"CCDC141"': 0.0, '"CCDC40"': 0.0, '"FAM193A"': 0.0, '"TUBA1A"': 0.0, '"ABAT"': 0.0, '"OAZ2"': 0.0, '"TIGD2"': 0.0, '"GAB1"': 0.0, '"ABHD14B"': 0.0, '"NAPA-AS1"': 0.0, '"FAM53C"': 0.0, '"ADAM19"': 0.0, '"LINC02664"': 0.0, '"PCDHB11"': 0.0, '"FGF8"': 0.0, '"NAALAD2"': 0.0, '"HEIH"': 0.0, '"LINC01840"': 0.0, '"DET1"': 0.0, '"TCL6"': 0.0, '"YJEFN3"': 0.0, '"ARHGEF33"': 0.0, '"PPIAP46"': 0.0, '"SDK1"': 0.0, '"FANCF"': 0.0, '"SELENOP"': 0.0, '"MATN2"': 0.0, '"IRS2"': 0.0, '"STARD4"': 0.0, '"NRARP"': 0.0, '"ZNF132"': 0.0, '"TLE2"': 0.0, '"OSER1-DT"': 0.0, '"ITM2C"': 0.0, '"TCAIM"': 0.0, '"FAM86C2P"': 0.0, '"SNX11"': 0.0, '"CST6"': 0.0, '"ZNF76"': 0.0, '"RHOB"': 0.0, '"CCDC62"': 0.0, '"HERPUD2-AS1"': 0.0, '"ARMH3"': 0.0, '"P2RX7"': 0.0, '"ZC3H10"': 0.0, '"CRTAM"': 0.0, '"STIM2-AS1"': 0.0, '"LINC02541"': 0.0, '"FRG1JP"': 0.0, '"BBS4"': 0.0, '"HCP5"': 0.0, '"CDKN1C"': 0.0, '"ZNF654"': 0.0, '"TMCC2"': 0.0, '"KANK3"': 0.0, '"AGBL5"': 0.0, '"NOTCH2NLC"': 0.0, '"RIMS2"': 0.0, '"PDK2"': 0.0, '"JOSD2"': 0.0, '"OR10D3"': 0.0, '"DPY19L1"': 0.0, '"CCDC71L"': 0.0, '"DALRD3"': 0.0, '"HLA-V"': 0.0, '"MAP3K10"': 0.0, '"YBX1P6"': 0.0, '"TRANK1"': 0.0, '"RAB9A"': 0.0, '"CRLF1"': 0.0, '"FMC1"': 0.0, '"RAB17"': 0.0, '"ZFP28"': 0.0, '"GORASP1"': 0.0, '"GAREM2"': 0.0, '"AKR1B10"': 0.0, '"LINC01679"': 0.0, '"ZDHHC18"': 0.0, '"ACVR1C"': 0.0, '"CTXN1"': 0.0, '"ZFYVE27"': 0.0, '"TRPM2-AS"': 0.0, '"CHIC2"': 0.0, '"MTND2P28"': 0.0, '"SORBS3"': 0.0, '"SLC40A1"': 0.0, '"RALGDS"': 0.0, '"HAGLROS"': 0.0, '"PRXL2B"': 0.0, '"TRAIP"': 0.0, '"PPP2R3B"': 0.0, '"ENKD1"': 0.0, '"CDR2"': 0.0, '"SPATA6L"': 0.0, '"LRRC75B"': 0.0, '"OXSM"': 0.0, '"PADI1"': 0.0, '"MT-TT"': 0.0, '"TTC30A"': 0.0, '"RPGR"': 0.0, '"EVC2"': 0.0, '"LHX6"': 0.0, '"LINC01139"': 0.0, '"WDR24"': 0.0, '"PITX1-AS1"': 0.0, '"ADA2"': 0.0, '"HIF3A"': 0.0, '"DNLZ"': 0.0, '"ZNF470"': 0.0, '"NEK3"': 0.0, '"ST13P7"': 0.0, '"PLEKHO1"': 0.0, '"CFAP410"': 0.0, '"ADTRP"': 0.0, '"ITPRIP"': 0.0, '"BMP4"': 0.0, '"ALG13"': 0.0, '"UMAD1"': 0.0, '"ZNF880"': 0.0, '"ZNF514"': 0.0, '"AMPD2"': 0.0, '"VSIR"': 0.0, '"SLC2A10"': 0.0, '"PARP10"': 0.0, '"ZNF879"': 0.0, '"ZNF117"': 0.0, '"NAT1"': 0.0, '"PLP2"': 0.0, '"LRRC37A3"': 0.0, '"USP20"': 0.0, '"UBAC2"': 0.0, '"MCMDC2"': 0.0, '"SESN2"': 0.0, '"FAM228B"': 0.0, '"PBX3"': 0.0, '"RNF223"': 0.0, '"LTBP1"': 0.0, '"TFE3"': 0.0, '"ADGRL3"': 0.0, '"ITGA1"': 0.0, '"LYSMD1"': 0.0, '"SMIM26"': 0.0, '"NPEPL1"': 0.0, '"TUBB3"': 0.0, '"PAX6"': 0.0, '"HS6ST1"': 0.0, '"AGO4"': 0.0, '"MFAP2"': 0.0, '"SECISBP2L"': 0.0, '"ANO7L1"': 0.0, '"NUAK2"': 0.0, '"B9D2"': 0.0, '"HDAC11"': 0.0, '"RPL13AP7"': 0.0, '"CXCR2"': 0.0, '"AIP"': 0.0, '"RPL12P38"': 0.0, '"LRTM1"': 0.0, '"ZBED2"': 0.0, '"ERF"': 0.0, '"DYNLT2"': 0.0, '"TAGAP-AS1"': 0.0, '"GATA2-AS1"': 0.0, '"GLMP"': 0.0, '"UST"': 0.0, '"RCBTB2"': 0.0, '"RTL8A"': 0.0, '"RNF32"': 0.0, '"MIF4GD-DT"': 0.0, '"MYL9"': 0.0, '"RAB40C"': 0.0, '"ELFN2"': 0.0, '"SETMAR"': 0.0, '"PROS1"': 0.0, '"ARID5A"': 0.0, '"SMIM20"': 0.0, '"TM7SF2"': 0.0, '"EHD3"': 0.0, '"KDM6B"': 0.0, '"COL27A1"': 0.0, '"ITGB6"': 0.0, '"MAPK7"': 0.0, '"BCKDHB"': 0.0, '"LINC01816"': 0.0, '"AP1G2"': 0.0, '"TXNRD3"': 0.0, '"H2AW"': 0.0, '"SERPINB7"': 0.0, '"LTBP2"': 0.0, '"WDR90"': 0.0, '"CAPNS2"': 0.0, '"ASCL2"': 0.0, '"SAP30L"': 0.0, '"RHOXF2"': 0.0, '"KIF3C"': 0.0, '"GRK4"': 0.0, '"BICRA"': 0.0, '"CXXC5"': 0.0, '"UPRT"': 0.0, '"NPIPB4"': 0.0, '"CNEP1R1"': 0.0, '"PYCR1"': 0.0, '"EDAR"': 0.0, '"NDUFB4"': 0.0, '"PODXL2"': 0.0, '"DKK1"': 0.0, '"NOVA2"': 0.0, '"PLK4"': 0.0, '"WWOX-AS1"': 0.0, '"LINC00683"': 0.0, '"HFE"': 0.0, '"NANOS1"': 0.0, '"NECTIN4"': 0.0, '"RPL12P13"': 0.0, '"CRYM-AS1"': 0.0, '"ZKSCAN4"': 0.0, '"ADA"': 0.0, '"TNFRSF11A"': 0.0, '"C2orf27A"': 0.0, '"OBSL1"': 0.0, '"LAX1"': 0.0, '"CATSPERB"': 0.0, '"SETBP1"': 0.0, '"GJB3"': 0.0, '"ATP8B2"': 0.0, '"ZNF385A"': 0.0, '"RPL9P32"': 0.0, '"FSD1L"': 0.0, '"CNKSR1"': 0.0, '"VAMP2"': 0.0, '"FAM241B"': 0.0, '"LINC01102"': 0.0, '"LINC01266"': 0.0, '"SOX21-AS1"': 0.0, '"LPP-AS2"': 0.0, '"CHTF18"': 0.0, '"PANK1"': 0.0, '"FA2H"': 0.0, '"NSA2P4"': 0.0, '"ANXA4"': 0.0, '"SUMF1"': 0.0, '"SPRY1"': 0.0, '"STK36"': 0.0, '"TNC"': 0.0, '"LINC01637"': 0.0, '"LASTR"': 0.0, '"RASSF3"': 0.0, '"KBTBD4"': 0.0, '"RIMKLA"': 0.0, '"RAB42"': 0.0, '"ARHGEF17"': 0.0, '"KLHDC3"': 0.0, '"RAB30"': 0.0, '"MLH3"': 0.0, '"ITGBL1"': 0.0, '"EVI5L"': 0.0, '"PPP1R3G"': 0.0, '"REEP1"': 0.0, '"ABHD17A"': 0.0, '"GSDME"': 0.0, '"NXT2"': 0.0, '"RBM43"': 0.0, '"BLCAP"': 0.0, '"YWHAQP5"': 0.0, '"LINC01322"': 0.0, '"CCPG1"': 0.0, '"JAZF1"': 0.0, '"FZD1"': 0.0, '"ZNF577"': 0.0, '"TEDC2"': 0.0, '"LINC00663"': 0.0, '"C1orf53"': 0.0, '"MYH7B"': 0.0, '"CKB"': 0.0, '"NTRK2"': 0.0, '"BDKRB2"': 0.0, '"SSPN"': 0.0, '"RELB"': 0.0, '"BMP8B"': 0.0, '"KHNYN"': 0.0, '"MAP3K6"': 0.0, '"ZNF45"': 0.0, '"ATP5PDP3"': 0.0, '"CADM1"': 0.0, '"LINC01415"': 0.0, '"ST3GAL1-DT"': 0.0, '"TAB1"': 0.0, '"IL1A"': 0.0, '"SMARCAL1"': 0.0, '"EPOP"': 0.0, '"LINC00960"': 0.0, '"MAU2"': 0.0, '"DYNC1LI2-DT"': 0.0, '"LOXL2"': 0.0, '"PWRN1"': 0.0, '"IFT74"': 0.0, '"LRRC61"': 0.0, '"SLC6A9"': 0.0, '"GBA"': 0.0, '"TNFSF13B"': 0.0, '"ZNF433"': 0.0, '"MBTPS1-DT"': 0.0, '"ACTBP2"': 0.0, '"SH2B3"': 0.0, '"NOD1"': 0.0, '"CA11"': 0.0, 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'"FLAD1"': 2.11676615932205e-05, '"RPS15AP29"': 2.1205779598075607e-05, '"OPRM1"': 2.1266046807996633e-05, '"VMA21"': 2.1266046807996633e-05, '"ASNSD1"': 2.1292262938256545e-05, '"DRD4"': 2.205381255436931e-05, '"NARS2"': 2.350041625954903e-05, '"INKA1"': 2.3654234632534966e-05, '"HCFC1R1"': 2.3654234632534966e-05, '"NR2F6"': 2.3654234632534966e-05, '"LINC01559"': 2.36549227165851e-05, '"CDK5"': 2.3732181017071506e-05, '"SAT2"': 2.3732181017071506e-05, '"NELFB"': 2.375893589888364e-05, '"IQANK1"': 2.3813619292373067e-05, '"IMPACT"': 2.3813619292373067e-05, '"PXMP4"': 2.3813619292373067e-05, '"KLRK1-AS1"': 2.3856502047835057e-05, '"RBP1"': 2.3856502047835057e-05, '"CENPM"': 2.392430265899621e-05, '"SYVN1"': 2.5067110676852302e-05, '"RHOV"': 2.532435145879753e-05, '"IFIT1"': 2.532435145879753e-05, '"PROSER2"': 2.532435145879753e-05, '"MAGEA3"': 2.532435145879754e-05, '"KBTBD3"': 2.5342864958809203e-05, '"TMEM45A"': 2.5446935517690716e-05, '"LEMD3"': 2.551925616959596e-05, '"NKX2-1"': 2.5550715525907843e-05, '"PPIL1"': 2.5550715525907856e-05, '"DYNLT1"': 2.628248292503885e-05, '"MDC1"': 2.6344932217617784e-05, '"HK1"': 2.6379532769580778e-05, '"MAP2K3"': 2.6582558509995783e-05, '"JADE1"': 2.669112315219052e-05, '"ACYP2"': 2.703341100861139e-05, '"RAB12"': 2.7122492590938863e-05, '"LAMTOR2"': 2.7133233705854513e-05, '"ABTB1"': 2.7264573768954354e-05, '"CDT1"': 2.7308784111887148e-05, '"TBC1D13"': 2.7342060181709954e-05, '"FOXRED2"': 2.7418010348881346e-05, '"UBQLN4"': 2.7852345196502554e-05, '"B3GALT1"': 2.7852345196502554e-05, '"MYO1C"': 2.7911686435495577e-05, '"AMBRA1"': 2.809442041356865e-05, '"NAGK"': 2.813104015305626e-05, '"GOLGA5"': 2.822354879096067e-05, '"BMP1"': 2.835472907732884e-05, '"TCEAL3"': 2.8421333259628218e-05, '"PLD1"': 2.848535304187762e-05, '"TNS4"': 2.849765141125053e-05, '"DTX2"': 2.8616983182096933e-05, '"CANT1"': 2.862780245740207e-05, '"PTK2B"': 2.8667815550285164e-05, '"ZNF169"': 2.8740648264778598e-05, '"BAHD1"': 2.89183148707136e-05, '"LINC01963"': 2.8978189132964965e-05, '"ACADS"': 2.8979425439379555e-05, '"CAPN10"': 2.900599902086517e-05, '"CRYZ"': 2.9029362191029497e-05, '"VRK3"': 2.9151559242135767e-05, '"CBX6"': 2.9182441787092572e-05, '"LMX1B"': 2.918961527649665e-05, '"NTN4"': 2.9212476762843096e-05, '"AKT1"': 2.9241767260164447e-05, '"SLC25A22"': 2.9292237606410974e-05, '"FAM171B"': 2.9346174150286e-05, '"NPRL2"': 2.938270030685043e-05, '"KLLN"': 2.9490718443355626e-05, '"ARNTL"': 2.9502161602617443e-05, '"HMGN1P26"': 2.95060829832571e-05, '"HOXB2"': 2.9545076701930468e-05, '"VPS16"': 2.956142442691419e-05, '"MIR320A"': 2.9571641359984075e-05, '"RAD51"': 2.9576713269889783e-05, '"PSMD10P2"': 2.958177333477776e-05, '"NECAB3"': 2.9593116771283973e-05, '"NRXN3"': 2.9679552002794218e-05, '"EIF3F"': 2.9686450237404224e-05, '"PMEPA1"': 2.9793354657408853e-05, '"DNAAF5"': 2.9822832484161582e-05, '"DCAF7"': 2.9837301052003357e-05, '"RPL34P1"': 2.9855983420541725e-05, '"CYHR1"': 2.985936263925305e-05, '"RPL5P3"': 2.988375754337012e-05, '"WASF3"': 2.9903464106713924e-05, '"ZNF580"': 2.991933344520746e-05, '"CTDSP2"': 2.9945825651253386e-05, '"LIPE-AS1"': 2.995047322115258e-05, '"COMMD10"': 3.000227643822832e-05, '"KDM3A"': 3.0027664161671358e-05, '"CRIP2"': 3.004215321358177e-05, '"GM2A"': 3.0059665324597456e-05, '"ABHD14A"': 3.009048007836443e-05, '"C1orf115"': 3.0107451565332827e-05, '"TCEAL1"': 3.010849396299175e-05, '"TEX261"': 3.010849396299175e-05, '"UBTD1"': 3.010849396299175e-05, '"FBF1"': 3.013264201552405e-05, '"LINC01854"': 3.0135781308655982e-05, '"PARS2"': 3.0145298101111867e-05, '"PPFIA3"': 3.0150992257713675e-05, '"RNF227"': 3.0154122769603667e-05, '"SLC29A2"': 3.016403916253011e-05, '"RUSC1"': 3.0170077331915744e-05, '"LTBP4"': 3.017301489090976e-05, '"PAPSS2"': 3.0176922358362184e-05, '"CEP250"': 3.0188494813297706e-05, '"IFI6"': 3.0195693435310744e-05, '"INSR"': 3.0200574772420043e-05, '"SQOR"': 3.022908094119167e-05, '"DENND3-AS1"': 3.0231301449207185e-05, '"VPS45"': 3.0231576394806605e-05, '"CD2AP-DT"': 3.0231822387437875e-05, '"TBC1D7"': 3.023335440169475e-05, '"MSH5"': 3.023792392822388e-05, '"OR7E14P"': 3.0242594659712456e-05, '"GRB14"': 3.0276669900165067e-05, '"GLB1"': 3.0287331494416237e-05, '"SMCR5"': 3.0290915019861004e-05, '"CDA"': 3.0301251581184894e-05, '"RBAK"': 3.030824273574754e-05, '"PAN2"': 3.0310895239813812e-05, '"CHN1"': 3.0315268872363776e-05, '"DHRS4"': 3.031557753657079e-05, '"MSTO1"': 3.0334499293553325e-05, '"CDC42BPG"': 3.0346423558574116e-05, '"TNFRSF14"': 3.0347101630367627e-05, '"PANX2"': 3.034777588310643e-05, '"STAT2"': 3.036282078815365e-05, '"SEC61G"': 3.0362820788153713e-05, '"UNC13D"': 3.0370718213893745e-05, '"NAIP"': 3.0374535801984047e-05, '"BCL7B"': 3.0374657709424237e-05, '"AAMDC"': 3.0380066868566626e-05, '"DLX6"': 3.038626698181253e-05, '"OAZ3"': 3.0402914490255458e-05, '"CERS6"': 3.0414319701012473e-05, '"DBT"': 3.041614157816702e-05, '"ELF4"': 3.042568377115196e-05, '"CARD9"': 3.043037824553462e-05, '"RAB3GAP1"': 3.043740751571382e-05, '"P2RY2"': 3.0447673713533388e-05, '"TMEM184B"': 3.0451428492458804e-05, '"ORMDL3"': 3.0462958931576567e-05, '"MREG"': 3.0469244996239044e-05, '"WIPF2"': 3.0512804164806223e-05, '"EFNA1"': 3.051837852204393e-05, '"ERP27"': 3.0523455684373304e-05, '"CDH8"': 3.0533236889784726e-05, '"MYH15"': 3.054402577985068e-05, '"CDCA4"': 3.055612912671604e-05, '"MAGEA12"': 3.055688161571648e-05, '"RTL8C"': 3.05669865740158e-05, '"SERINC2"': 3.0584623511882964e-05, '"MAN1B1-DT"': 3.058552725324609e-05, '"ST3GAL6"': 3.0602595340310635e-05, '"SNHG6"': 3.060641201887151e-05, '"IMMP2L"': 3.062087731203157e-05, '"KCTD2"': 3.0620912733511426e-05, '"FASTKD3"': 3.0624306385393676e-05, '"PTPDC1"': 3.062885498373353e-05, '"FAM210B"': 3.0634141540895695e-05, '"ZNF865"': 3.063429611951315e-05, '"TINF2"': 3.064006653268822e-05, '"LINC00320"': 3.064623852706772e-05, '"C16orf91"': 3.064834910084419e-05, '"MT-TA"': 3.065413401986426e-05, '"LRRC45"': 3.0667209870617205e-05, '"AXIN1"': 3.066830838898171e-05, '"NEU1"': 3.0669677835791566e-05, '"NCKIPSD"': 3.0672016113947816e-05, '"MYOM3"': 3.069158737882745e-05, '"CPNE2"': 3.069879190388637e-05, '"PSPN"': 3.070195795135311e-05, '"IL18"': 3.070341604186487e-05, '"MT-TE"': 3.0707379440287e-05, '"HBM"': 3.070941325816115e-05, '"BCAR1"': 3.071203064422834e-05, '"CDHR3"': 3.072024098829139e-05, '"FOXF2"': 3.0722545863126606e-05, '"SLC41A3"': 3.072406862239605e-05, '"CCDC15-DT"': 3.0725680488198344e-05, '"SGO2"': 3.072725069983614e-05, '"ISOC1"': 3.074025253485797e-05, '"SAMD4B"': 3.074268290557357e-05, '"CTBP1"': 3.074649026638174e-05, '"TNNT1"': 3.0746735015950095e-05, '"TTC28"': 3.0750505022295456e-05, '"SNAPC1"': 3.076973610736256e-05, '"MCRIP1"': 3.0773478878554044e-05, '"CSRNP1"': 3.07774323688368e-05, '"ZNF8-DT"': 3.0782558730400004e-05, '"METAP1D"': 3.078359772727427e-05, '"BRSK2"': 3.078458284889232e-05, '"RHNO1"': 3.079092579234358e-05, '"MORN1"': 3.0794113247668056e-05, '"DMD"': 3.079808679880644e-05, '"PCOLCE"': 3.079975674128389e-05, '"CCDC9B"': 3.080133666864222e-05, '"PLCG1"': 3.0802620108570674e-05, '"TUBD1"': 3.0816733191394565e-05, '"NLGN2"': 3.081882933625339e-05, '"ANOS1"': 3.082419771521689e-05, '"SLC4A2"': 3.084399710854188e-05, '"SIRT5"': 3.084656910818693e-05, '"POLR2H"': 3.084861610297278e-05, '"TGFB1I1"': 3.085075382952701e-05, '"MIR210HG"': 3.085806891816116e-05, '"DBF4B"': 3.086090369038161e-05, '"CCDC88B"': 3.0875207425897955e-05, '"LINC02057"': 3.087698672853315e-05, '"PIP4P2"': 3.0882153209682456e-05, '"RAB35"': 3.0886261369693015e-05, '"AAGAB"': 3.0891007471415914e-05, '"UQCRB-AS1"': 3.0891360582086955e-05, '"GDI1"': 3.0892389288386915e-05, '"CMTM4"': 3.089408106866767e-05, '"PGBD2"': 3.089476205511272e-05, '"N4BP2L2-IT2"': 3.089980784545247e-05, '"C19orf44"': 3.0900327265612856e-05, '"CIAO2A"': 3.09022242678701e-05, '"OPN3"': 3.090326378429516e-05, '"MEGF6"': 3.090683472741623e-05, '"WWC1"': 3.090702644083731e-05, '"ALS2CL"': 3.091109608147952e-05, '"NOP10"': 3.091138713533822e-05, '"DPPA2"': 3.092033855740853e-05, '"HOXC13"': 3.0921600341511886e-05, '"GSK3A"': 3.093725684801391e-05, '"TASOR"': 3.093810210600065e-05, '"ALDH3B1"': 3.094031958215405e-05, '"FOXD2"': 3.0948765264222e-05, '"SPATA2"': 3.0951285767607124e-05, '"GAS2L1"': 3.095198511630811e-05, '"JAKMIP3"': 3.095757664422293e-05, '"MMAA"': 3.0957669547741884e-05, '"SNAP47"': 3.096086226458333e-05, '"ITGB8-AS1"': 3.0961798152208466e-05, '"TMEM256"': 3.097286888047438e-05, '"KRT18P59"': 3.0975834579669405e-05, '"NRBP2"': 3.097919107628416e-05, '"TMEM102"': 3.09890972064233e-05, '"GIPC1"': 3.09918585599888e-05, '"RPL21P10"': 3.099220954743577e-05, '"TIGD1"': 3.0995679826947846e-05, '"TMCO6"': 3.100173611115658e-05, '"MANBA"': 3.1004057942422585e-05, '"BEND6"': 3.1005435303413065e-05, '"MRPL45"': 3.100648038790894e-05, '"PDE6D"': 3.100745724684936e-05, '"HILPDA"': 3.101332985154584e-05, '"ZNF268"': 3.1013452662185624e-05, '"LMF2"': 3.1015680160042526e-05, '"IPO13"': 3.102060710713725e-05, '"SH3BP5L"': 3.102869737310251e-05, '"METTL25B"': 3.102986756278915e-05, '"RMI2"': 3.103118091198665e-05, '"PISD"': 3.103679789551824e-05, '"E2F1"': 3.103711176055428e-05, '"UBA3"': 3.103859645938441e-05, '"DHCR7"': 3.104664175606624e-05, '"ZNF446"': 3.1046895470726894e-05, '"CITED2"': 3.1047079664272055e-05, '"GABPA"': 3.1048046265533835e-05, '"CASC2"': 3.104873696316948e-05, '"DUSP23"': 3.105230990579142e-05, '"VDR"': 3.105336663170316e-05, '"KIF26A"': 3.1057522645979905e-05, '"HERC1"': 3.1068233963217785e-05, '"EPHX1"': 3.107648549288519e-05, '"TBC1D22A-AS1"': 3.1077277195177965e-05, '"CHST5"': 3.1078089531291394e-05, '"RHOXF2B"': 3.107896506897482e-05, '"TDRKH-AS1"': 3.1082632472907216e-05, '"ARVCF"': 3.108362341665337e-05, '"TOMM5"': 3.108869076758613e-05, '"DVL1"': 3.109016362129162e-05, '"TCAF1"': 3.109102595352327e-05, '"GLIPR1"': 3.109466096487061e-05, '"NCOA1"': 3.1097547269982143e-05, '"FAM189B"': 3.110140090958314e-05, '"WDR74"': 3.110159345669508e-05, '"XKR8"': 3.110197697345216e-05, '"ZRANB1"': 3.110583113625266e-05, '"GKAP1"': 3.1107652411522286e-05, '"PER1"': 3.111717658413274e-05, '"CAPN1"': 3.111890645360715e-05, '"PKIB"': 3.112021155415624e-05, '"LPAR4"': 3.112755068173907e-05, '"TRAFD1"': 3.1129382373552505e-05, '"RAPGEF3"': 3.114798379395685e-05, '"TAF1C"': 3.114874030099153e-05, '"PRR14"': 3.115173709819811e-05, '"FYN"': 3.115448413257823e-05, '"HMGCS1"': 3.115717823834771e-05, '"PRRX2"': 3.1161726709034815e-05, '"C20orf96"': 3.116364363928723e-05, '"MUC4"': 3.116475969647453e-05, '"CRACDL"': 3.116755391324157e-05, '"TCF7L1"': 3.1173201739162215e-05, '"IFITM10"': 3.117906834992552e-05, '"CEACAM19"': 3.1179275240328116e-05, '"ATXN7L2"': 3.1179984279869775e-05, '"LZTR1"': 3.118200169466327e-05, '"POLD1"': 3.1182035217384836e-05, '"C14orf132"': 3.1188952116243886e-05, '"CTHRC1"': 3.1189431493083616e-05, '"C1orf112"': 3.1191975854972655e-05, '"FASTKD5"': 3.11925436776711e-05, '"ABT1"': 3.119310453921986e-05, '"VEGFB"': 3.119444866369337e-05, '"PPP1R13L"': 3.119653323480991e-05, '"IGFL2-AS1"': 3.119905152860885e-05, '"GBP1"': 3.120029294046544e-05, '"UCKL1"': 3.1210324501078516e-05, '"HLA-DPB1"': 3.121422489186762e-05, '"VPS9D1"': 3.121689491395696e-05, '"TPRG1"': 3.1220483175010557e-05, '"MRPS36"': 3.122069598192496e-05, '"MOV10"': 3.122117822399156e-05, '"C16orf95"': 3.1222842415760854e-05, '"SNHG19"': 3.1226553969830934e-05, '"LINC01931"': 3.1229500809740394e-05, '"NUP93"': 3.123196116532354e-05, '"FOXJ2"': 3.1233108072919473e-05, '"ZNF74"': 3.123722971477788e-05, '"HAGLR"': 3.125632921649632e-05, '"CBWD6"': 3.125698238771557e-05, '"SREBF1"': 3.126116755591601e-05, '"LINC02582"': 3.126166816706608e-05, '"ZNF165"': 3.126472751430708e-05, '"IQCH-AS1"': 3.126688661242637e-05, '"CUEDC1"': 3.127150985161103e-05, '"ZBTB10"': 3.127289824692753e-05, '"PRKCH"': 3.128802629988007e-05, '"ADAM15"': 3.129822394126764e-05, '"INPP5E"': 3.1308484191392485e-05, '"OVOL1"': 3.1309045657718194e-05, '"TBC1D20"': 3.131167386728794e-05, '"RNPEPL1"': 3.1313434636187355e-05, '"BLOC1S6P1"': 3.131859732125571e-05, '"BOLA3-AS1"': 3.131877048445988e-05, '"IKBKE"': 3.132222417272333e-05, '"ALPK1"': 3.1323745615984534e-05, '"SREK1IP1P1"': 3.132837689891087e-05, '"CCDC92"': 3.132961190372491e-05, '"CRPPA"': 3.133309280965706e-05, '"RTL6"': 3.134089484715586e-05, '"CORO7"': 3.134572108084446e-05, '"GATA3"': 3.135395894898744e-05, '"PCIF1"': 3.135689493218926e-05, '"PDE8A"': 3.1364170948357595e-05, '"LINC01687"': 3.1369742940737465e-05, '"PTRHD1"': 3.137364911985921e-05, '"LATS2"': 3.137674422644553e-05, '"KLHL24"': 3.13771754540928e-05, '"PITPNM1"': 3.1379162027395365e-05, '"ZBTB47"': 3.1379583631031686e-05, '"ZFHX3"': 3.1382519691983544e-05, '"DOCK9"': 3.1390405217945606e-05, '"ROR2"': 3.139462092376611e-05, '"TINAGL1"': 3.1403683725002644e-05, '"HEBP1"': 3.1404116451853585e-05, '"PRECSIT"': 3.140608783392842e-05, '"WAC-AS1"': 3.14100483209892e-05, '"TP53I13"': 3.1411291333892586e-05, '"PTPRU"': 3.1412513785616946e-05, '"MTCO1P40"': 3.14145930218571e-05, '"LINC01405"': 3.1419968239907344e-05, '"ASB7"': 3.1427412888917564e-05, '"CSPG4P12"': 3.1429807454485314e-05, '"LRRC3"': 3.14313311525607e-05, '"RASSF10"': 3.143473099629647e-05, '"GAS8"': 3.143876022906677e-05, '"UBE2I"': 3.1454749470299624e-05, '"ANKRD28"': 3.145523973714549e-05, '"LINC02273"': 3.1459769139379985e-05, '"TMEM250"': 3.146218936565154e-05, '"IL4R"': 3.146549650780264e-05, '"LINC02870"': 3.146561338471396e-05, '"LYPD1"': 3.1473749275835016e-05, '"CXCL8"': 3.148804886559135e-05, '"PTPRB"': 3.149077865726821e-05, '"HSP90AA4P"': 3.149373207634992e-05, '"SH3D21"': 3.150174250746017e-05, '"TIAM2"': 3.1509561722928e-05, '"CCN2"': 3.1511062572667456e-05, '"RAD9A"': 3.151474406486248e-05, '"GTF3C5"': 3.151684674209403e-05, '"NIPSNAP3A"': 3.1521872068967405e-05, '"CCS"': 3.153109562692186e-05, '"TRG-AS1"': 3.154584388772286e-05, '"SURF1"': 3.155655126856665e-05, '"ZNF250"': 3.155770279395568e-05, '"ZNF25"': 3.156341769755613e-05, '"SYT7"': 3.156428893601188e-05, '"SH3BGRL2"': 3.15658551269066e-05, '"TMEM231"': 3.156842835337538e-05, '"SPDYE3"': 3.1575704888676706e-05, '"POLE2"': 3.159497081160649e-05, '"SH2B1"': 3.159957137361181e-05, '"TMEM126A"': 3.162168699276014e-05, '"SMIM29"': 3.163110086216561e-05, '"SMCO4"': 3.164081442282183e-05, '"YPEL2"': 3.1641683443173715e-05, '"ZNF462"': 3.16690808168254e-05, '"ZNRF1"': 3.172890948758356e-05, '"WNT7A"': 3.1784736627005717e-05, '"SLC52A1"': 3.1800919226727946e-05, '"TRIM52-AS1"': 3.1831218587225815e-05, '"TANGO2"': 3.184660463598838e-05, '"SLC38A10"': 3.701310097673099e-05, '"AKR7A2"': 3.817040327653609e-05, '"MIXL1"': 3.853872713817447e-05, '"ACSL4"': 3.8737407247679866e-05, '"NEK1"': 3.875733890309952e-05, '"FUOM"': 3.876086589592319e-05, '"HEY1"': 3.898743070064991e-05, '"DLK2"': 3.941197206473911e-05, '"PATZ1"': 3.946592595662319e-05, '"TRAPPC2B"': 3.968949548980198e-05, '"NEK8"': 3.9996335939051426e-05, '"PLD5"': 4.0134435718932945e-05, '"TEX9"': 4.024540817475344e-05, '"IFRD2"': 4.044447861914603e-05, '"CRNDE"': 4.048508953504771e-05, '"HSPA2"': 4.064502975279487e-05, '"C19orf54"': 4.1136700439214036e-05, '"FAM120C"': 4.12377641566558e-05, '"LAGE3"': 4.215189154818845e-05, '"TUBA1C"': 4.2335323186441e-05, '"TRIB2"': 4.476269763723625e-05, '"JUND"': 4.505568501435231e-05, '"UBL4A"': 4.5222056176424184e-05, '"SPATC1L"': 4.544095628159059e-05, '"PDLIM3"': 4.635938788100662e-05, '"THAP2"': 4.654101550665846e-05, '"KCTD11"': 4.6708929105269914e-05, '"CLDN11"': 4.676128879229621e-05, '"RHBDF1"': 4.7001993865170913e-05, '"FADS2"': 4.702924369263588e-05, '"YEATS4"': 4.719017127110547e-05, '"THOC7"': 4.7424718918545245e-05, '"IQCC"': 4.745958725512102e-05, '"L3MBTL2"': 4.8303424164768184e-05, '"CAPZB"': 4.92223013687409e-05, '"RAB11B"': 4.924179450321743e-05, '"S100A13"': 4.961697008038483e-05, '"BASP1"': 4.9993676498897435e-05, '"ACVR2B"': 5.0134221353704604e-05, '"STYX"': 5.127209871324254e-05, '"FAH"': 5.1402612514431645e-05, '"CNOT6L"': 5.141033754793486e-05, '"MRPL14"': 5.14160622405891e-05, '"IL6R"': 5.150016914722894e-05, '"APPL1"': 5.172077647851101e-05, '"ARL9"': 5.1771285097556805e-05, '"MSR1"': 5.182173476771968e-05, '"AP1S2"': 5.1879346980240434e-05, '"PBXIP1"': 5.1884974062498954e-05, '"ZNF598"': 5.203381822063371e-05, '"TLE3"': 5.2460817862109684e-05, '"FAM83A"': 5.2939507503814055e-05, '"MBD2"': 5.306063350111619e-05, '"PPP1R21"': 5.3181358021448735e-05, '"TPRA1"': 5.440291301976687e-05, '"KIAA2012-AS1"': 5.4609644085645026e-05, '"PFKP"': 5.4786182558063115e-05, '"SWSAP1"': 5.478706949185233e-05, '"ZNF524"': 5.486942816072799e-05, '"CSRP1"': 5.493681507732156e-05, '"TRDN"': 5.499130078398796e-05, '"TMEM179B"': 5.510301684826954e-05, '"DOCK6"': 5.520646326120147e-05, '"PBX4"': 5.5255669171624944e-05, '"PIAS2"': 5.5283166099638735e-05, '"IRAK1"': 5.5340276202930646e-05, '"COMMD6"': 5.5528521086723644e-05, '"FBRSL1"': 5.574964366573086e-05, '"TXNRD2"': 5.579579395965451e-05, '"FAM107A"': 5.5823372870991154e-05, '"COL5A1"': 5.600710080861485e-05, '"MKNK2"': 5.605871993047833e-05, '"PHRF1"': 5.6087879022148913e-05, '"DARS1-AS1"': 5.6152204052326285e-05, '"SH3BP1"': 5.6236136791475264e-05, '"UNC45A"': 5.627341420474621e-05, '"LINC01151"': 5.63174776862427e-05, '"FBXO42"': 5.6473424519793165e-05, '"FAM107B"': 5.647497425557699e-05, '"ZNF628"': 5.6521054639193726e-05, '"ARAF"': 5.6616105687641325e-05, '"RNF10"': 5.682441153201165e-05, '"LRRC23"': 5.734955982577926e-05, '"KRT16"': 5.739823699377112e-05, '"TTC3P1"': 5.7405059444499206e-05, '"NEFL"': 5.745426326072403e-05, '"CDK19"': 5.755012848469933e-05, '"PDPK1"': 5.759046060520946e-05, '"SHKBP1"': 5.77169001181963e-05, '"ATP1A1-AS1"': 5.771721183399942e-05, '"TCP11L1"': 5.773923608220691e-05, '"MT1F"': 5.7754942750015304e-05, '"LSM14A"': 5.7771771724496345e-05, '"CTF1"': 5.778624238274635e-05, '"MAPK12"': 5.7823170486586374e-05, '"NKX3-1"': 5.78748424098743e-05, '"BTBD6"': 5.789100350390686e-05, '"MT-TY"': 5.795265298372581e-05, '"LDOC1"': 5.8029239243266626e-05, '"SOX15"': 5.814169545124565e-05, '"C15orf39"': 5.815089375475331e-05, '"KCTD1"': 5.816711033595957e-05, '"PLCXD2"': 5.817013426705993e-05, '"COX14"': 5.820507180672444e-05, '"ROM1"': 5.8367224261962115e-05, '"NRGN"': 5.841848058038832e-05, '"MAFK"': 5.8428096239386195e-05, '"FAM83A-AS1"': 5.8665064289863196e-05, '"RABGGTA"': 5.8683816171122806e-05, '"HHLA3"': 5.872328834480871e-05, '"SLC25A23"': 5.8787266250351334e-05, '"POLR3GL"': 5.8905568534067365e-05, '"C4orf48"': 5.896542170047349e-05, '"GMPPA"': 5.9032877345232116e-05, '"MAPK14"': 5.9042755025441726e-05, '"MESP1"': 5.906310315645454e-05, '"OR10K1"': 5.907665255606751e-05, '"ABCA2"': 5.9123930284474484e-05, '"BORCS6"': 5.9160430401837444e-05, '"CARF"': 5.920834520943335e-05, '"NCAM1"': 5.924937132959457e-05, '"ARFGEF3"': 5.9251013515695906e-05, '"MAP1A"': 5.929537620903034e-05, '"ETAA1"': 5.9305831058452363e-05, '"RBBP8NL"': 5.931942797026107e-05, '"CPTP"': 5.934840528358891e-05, '"CES1"': 5.948780322499299e-05, '"SNAPC3"': 5.9542809175929183e-05, '"PLSCR1"': 5.9623765912243914e-05, '"ARHGEF18"': 5.964834371784061e-05, '"ITPKC"': 5.9662878334016236e-05, '"LSP1P4"': 5.9674279567777665e-05, '"RAB36"': 5.9730494134032546e-05, '"MLLT3"': 5.973392657023115e-05, '"SPINK5"': 5.974407336716116e-05, '"ERG28"': 5.9796373755806755e-05, '"PAX5"': 5.982424762202014e-05, '"CASP1"': 5.989851378091027e-05, '"TSEN54"': 5.990085749895519e-05, '"SMOX"': 5.9931614804490405e-05, '"DYNLT3"': 5.993380253323903e-05, '"CAMKK1"': 6.010584563838184e-05, '"TMEM79"': 6.0115023850737286e-05, '"CUEDC2"': 6.0119157739467706e-05, '"SH3BGRL"': 6.013900865656445e-05, '"MLXIP"': 6.019663371789788e-05, '"RCHY1"': 6.029262932133991e-05, '"SLC26A6"': 6.033408873079233e-05, '"LINC02511"': 6.040483882773931e-05, '"ZNF23"': 6.040698148302807e-05, '"PDLIM4"': 6.042222670955944e-05, '"ZCCHC9"': 6.051428769673674e-05, '"FAM200B"': 6.05358000052254e-05, '"SORBS1"': 6.053700524586441e-05, '"SHFL"': 6.054618219299507e-05, '"SLC25A51P4"': 6.0586340084018745e-05, '"IDH3G"': 6.06214433623923e-05, '"ARHGAP22"': 6.065231977676447e-05, '"TBC1D10A"': 6.0653328338185786e-05, '"CASK"': 6.076256377970486e-05, '"IFI35"': 6.080491796044056e-05, '"TFPI2"': 6.0834197871310144e-05, '"PTPN21"': 6.091914399459566e-05, '"RGL3"': 6.0961164246631705e-05, '"TRAK1"': 6.1003790509851424e-05, '"MAP3K13"': 6.102511607437324e-05, '"MCEE"': 6.102841688792749e-05, '"ZNF324"': 6.103843755566762e-05, '"GATD1"': 6.106746628652511e-05, '"CACNB3"': 6.108932184770789e-05, '"HOXA4"': 6.114213129118707e-05, '"FOXP4"': 6.121084302395088e-05, '"CREB1"': 6.121211402467571e-05, '"PRKAA2"': 6.125051505812228e-05, '"FOXD1"': 6.126878573302177e-05, '"ATXN2L"': 6.12758459585575e-05, '"SLC25A1"': 6.13116869297305e-05, '"THNSL1"': 6.136646771293659e-05, '"SDHB"': 6.13705348866631e-05, '"DANT2"': 6.139037795767708e-05, '"MDFI"': 6.153371437542215e-05, '"NCK2"': 6.156944457323427e-05, '"ZNF213"': 6.157049436610562e-05, '"ERG"': 6.161307197737395e-05, '"FBXO33"': 6.161556031186621e-05, '"MAB21L3"': 6.162665712060108e-05, '"PLAC8"': 6.16354111674283e-05, '"HES2"': 6.16551856376718e-05, '"SLC9A3"': 6.16639425579093e-05, '"CHMP6"': 6.170964995348365e-05, '"MAML1"': 6.175008962479365e-05, '"VAV2"': 6.177597904971852e-05, '"GNAS-AS1"': 6.179167293830461e-05, '"NUPR2"': 6.179417556632854e-05, '"CCDC51"': 6.181735674998877e-05, '"SLC2A8"': 6.183972970835101e-05, '"MRPS6"': 6.18535566035664e-05, '"RARG"': 6.187705079904438e-05, '"SELENOO"': 6.188992894479311e-05, '"FHL2"': 6.189666215414523e-05, '"BOLA1"': 6.191872467844835e-05, '"ESCO1"': 6.191985714789964e-05, '"AMZ2P1"': 6.19328927859059e-05, '"UBQLN2"': 6.19481657566068e-05, '"BNC1"': 6.199137844043613e-05, '"ANKMY2"': 6.19957159087736e-05, '"UAP1L1"': 6.201410971673761e-05, '"DYNC2I1"': 6.203507185454723e-05, '"AJAP1"': 6.204235551594282e-05, '"PI4KB"': 6.20463679873449e-05, '"WBP2"': 6.207104325025327e-05, '"NDST1"': 6.207642533216346e-05, '"LINC01902"': 6.209679738285713e-05, '"TMEM121"': 6.211515336084182e-05, '"C18orf32"': 6.21299162160354e-05, '"C10orf88"': 6.213634132089965e-05, '"ZNF629"': 6.215935654631888e-05, '"MAML2"': 6.221205038908472e-05, '"MT-TM"': 6.223803261864425e-05, '"ACP5"': 6.229876127591114e-05, '"TAF1A"': 6.230677329662045e-05, '"DTWD2"': 6.230784566884204e-05, '"TMEM70"': 6.234068304902647e-05, '"GJD2"': 6.236237406582099e-05, '"MORC3"': 6.238748438420596e-05, '"SOX11"': 6.242323751182444e-05, '"EFNB1"': 6.244710012159677e-05, '"DNA2"': 6.24534067763113e-05, '"CEP120"': 6.247136640266256e-05, '"STC1"': 6.252993350819284e-05, '"MT-TL1"': 6.254912853770947e-05, '"ARL17B"': 6.264998685028945e-05, '"GALM"': 6.266151875520278e-05, '"TKFC"': 6.270581114430525e-05, '"LRRC20"': 6.270967094516001e-05, '"RAB11FIP4"': 6.28041367817532e-05, '"B3GAT2"': 6.283655877178698e-05, '"CRLS1"': 6.286933639821965e-05, '"SMC6"': 6.291751991772982e-05, '"GLCCI1"': 6.295141819513206e-05, '"WDR53"': 6.304812064367445e-05, '"ACSF3"': 6.315991487296738e-05, '"TBC1D19"': 6.342147228066472e-05, '"GDE1"': 6.414558054956844e-05, '"UBE2D1"': 6.419259069040781e-05, '"PPTC7"': 6.517269527060283e-05, '"CPEB1"': 6.550902021173581e-05, '"DUSP9"': 6.606268109354551e-05, '"REXO1"': 6.735276321343187e-05, '"MAN1A1"': 6.769968451341317e-05, '"PLEKHA4"': 6.821962279061105e-05, '"FCHO2"': 6.852609460962806e-05, '"ZKSCAN2"': 6.878740313801181e-05, '"RAB11FIP5"': 6.955333745794596e-05, '"CREB3L2"': 6.98264699850761e-05, '"CNTRL"': 6.995742593455304e-05, '"OXLD1"': 7.039251770691914e-05, '"ELP2"': 7.205550696412233e-05, '"AP1M1"': 7.258502408611888e-05, '"ZMYND8"': 7.271256696472562e-05, '"HES4"': 7.413211363751802e-05, '"NDUFA2"': 7.450657251682234e-05, '"PRPF40B"': 7.546218056774426e-05, '"SENP7"': 7.579287975959559e-05, '"GTF2IRD1"': 7.632116194683131e-05, '"NAT14"': 7.713994307016983e-05, '"RAB20"': 7.720497080597152e-05, '"SMIM4"': 7.765906733590497e-05, '"ARHGAP42"': 7.791831712904143e-05, '"SRC"': 7.825578114182603e-05, '"MBD3"': 7.835043757826459e-05, '"MRPS2"': 8.02415043428281e-05, '"TPD52L1"': 8.042261021624678e-05, '"FDXACB1"': 8.052448138147666e-05, '"ID1"': 8.070257408420093e-05, '"ZNF280B"': 8.087495790391859e-05, '"MINDY2"': 8.107562293231969e-05, '"SBNO2"': 8.109280582853116e-05, '"SLC2A11"': 8.111825722425076e-05, '"TMEM40"': 8.116897273546079e-05, '"LINC01962"': 8.136506426051155e-05, '"SUCLG2"': 8.164369103150995e-05, '"CCNI"': 8.170099422482318e-05, '"UBE2C"': 8.195426107289373e-05, '"GMPR2"': 8.231011255017882e-05, '"NRSN2-AS1"': 8.232651208261943e-05, '"SLMAP"': 8.24203088458312e-05, '"GCAT"': 8.244914363007675e-05, '"PDIA5"': 8.247137671078356e-05, '"CRACR2A"': 8.248129243207393e-05, '"PSD3"': 8.250001086416508e-05, '"ECH1"': 8.250584298536548e-05, '"RPSAP48"': 8.269354240163232e-05, '"ATP13A2"': 8.306880154440233e-05, '"NEDD9"': 8.325454635371105e-05, '"CDK5RAP2"': 8.329479166393283e-05, '"FBXO8"': 8.372710180489269e-05, '"TSPO"': 8.395136998923402e-05, '"ZBED4"': 8.420926150463098e-05, '"UCA1"': 8.426754378573085e-05, '"SLITRK2"': 8.432434236156018e-05, '"RAVER1"': 8.43333666977683e-05, '"FAM76B"': 8.440357974387431e-05, '"DPM3"': 8.456120550108767e-05, '"CCDC136"': 8.46627924376799e-05, '"PDXK"': 8.529032647898994e-05, '"C1orf21"': 8.536107656524565e-05, '"MT-TS1"': 8.537177289006246e-05, '"DCAF6"': 8.54453488669986e-05, '"HAUS7"': 8.548991916877292e-05, '"SPA17"': 8.557998743979328e-05, '"NRAV"': 8.57637332589008e-05, '"TCF3"': 8.594210906178716e-05, '"GSS"': 8.604435115858415e-05, '"ERRFI1"': 8.620366717701333e-05, '"FBXW5"': 8.624324162338105e-05, '"DOP1B"': 8.639707348357664e-05, '"HAAO"': 8.651706982541966e-05, '"ADARB1"': 8.670284664750243e-05, '"PFKFB3"': 8.672914623821159e-05, '"SRGAP2"': 8.678059231197981e-05, '"GPM6B"': 8.698677322116632e-05, '"KLHL7"': 8.700299848757052e-05, '"ILRUN-AS1"': 8.715901949213125e-05, '"EFCAB1"': 8.716354536271993e-05, '"AKT1S1"': 8.724663606065393e-05, '"OBSCN"': 8.746916506751959e-05, '"TRIOBP"': 8.747282642953206e-05, '"ZDHHC7"': 8.756493443309609e-05, '"PTPN6"': 8.785118994560345e-05, '"MID1IP1"': 8.802873531247926e-05, '"CLEC11A"': 8.808529884609504e-05, '"CARM1"': 8.822669827585198e-05, '"MAFF"': 8.84547475160065e-05, '"SH3RF2"': 8.851048330236139e-05, '"AKR1A1"': 8.853578914080392e-05, '"SLC25A46"': 8.871991098156979e-05, '"ZFC3H1"': 8.875569642591673e-05, '"QSOX1"': 8.87984596372198e-05, '"SDAD1P1"': 8.897199669848962e-05, '"LINC02298"': 8.905551809505478e-05, '"BRAT1"': 8.911990481530444e-05, '"TRIM8"': 8.91665588697229e-05, '"BIN3"': 8.9190330451241e-05, '"HNF4A"': 8.930609842821351e-05, '"LINC01234"': 8.934882361256831e-05, '"PCED1A"': 8.939319159719028e-05, '"MAZ"': 8.940887599512761e-05, '"C4orf46"': 8.955869744752154e-05, '"HMGB1P20"': 8.967634085099488e-05, '"TONSL"': 8.970719819897505e-05, '"MTND4P12"': 8.973838764339724e-05, '"OTULINL"': 8.992989700466958e-05, '"ZFP30"': 8.994411863465061e-05, '"HNRNPCP3"': 8.996733199670262e-05, '"ULK1"': 8.998135032604948e-05, '"CDK14"': 9.000431339581138e-05, '"MELTF-AS1"': 9.001065602930454e-05, '"NCK1"': 9.012825529678355e-05, '"C1QTNF6"': 9.022503324124382e-05, '"PSMA5"': 9.024408740354607e-05, '"CLIC4"': 9.027967857536168e-05, '"ZNF146"': 9.041372074579939e-05, '"ZNF184"': 9.046191993691752e-05, '"ZFP36L1"': 9.053550717329228e-05, '"KHK"': 9.053808014465877e-05, '"WARS2"': 9.058536644192925e-05, '"JMJD6"': 9.065484945897635e-05, '"IVL"': 9.069718767802659e-05, '"PRELID2"': 9.071881766862993e-05, '"XYLB"': 9.079397849444085e-05, '"BIK"': 9.079884249666155e-05, '"H2BC4"': 9.08624651646754e-05, '"RPL21P34"': 9.103281261857495e-05, '"KCTD15"': 9.112088604982712e-05, '"NUDT8"': 9.116408509361217e-05, '"ZNF195"': 9.126807884472676e-05, '"TBC1D22A"': 9.13171523459363e-05, '"KBTBD7"': 9.137359108924135e-05, '"TMTC4"': 9.141718456217527e-05, '"NRBP1"': 9.162464924049047e-05, '"DNHD1"': 9.16282587710843e-05, '"YY1AP1"': 9.164002596833764e-05, '"ARHGEF7"': 9.17305165182919e-05, '"NAP1L1P1"': 9.18020105045707e-05, '"GNAI2"': 9.185658590719054e-05, '"LTBP3"': 9.200404208758027e-05, '"ULK2"': 9.201895367950006e-05, '"EEF2K"': 9.219978767173361e-05, '"MAN2B1"': 9.225746128548726e-05, '"FAM126B"': 9.228468538102751e-05, '"UIMC1"': 9.251825755920593e-05, '"C19orf81"': 9.255604315267097e-05, '"DCTN2"': 9.258327043227085e-05, '"OGDH"': 9.264971232542914e-05, '"SLC16A4"': 9.273281510590135e-05, '"NFKBIL1"': 9.274584282351476e-05, '"TRAF4"': 9.278899564899244e-05, '"LINC01772"': 9.294008961831871e-05, '"MAPK8"': 9.297757414473726e-05, '"ZNF407-AS1"': 9.29953829044278e-05, '"AMDHD2"': 9.299911928330488e-05, '"CBWD3"': 9.326221874276708e-05, '"NUP62"': 9.326454191554115e-05, '"GPR153"': 9.330841713371325e-05, '"KRT4"': 9.330971957907539e-05, '"C16orf74"': 9.334220571667528e-05, '"ZDHHC8"': 9.336464330225033e-05, '"DPCD"': 9.34793513790509e-05, '"MCM3AP"': 9.351912657517495e-05, '"ITGA3"': 9.366173383642729e-05, '"BOK"': 9.383312088249547e-05, '"WDR54"': 9.38439734635563e-05, '"ARMC2"': 9.396286468634006e-05, '"MVK"': 9.4012739939234e-05, '"FBXL19"': 9.418752809676265e-05, '"MPPE1"': 9.437399436574548e-05, '"AGRN"': 9.452284901155599e-05, '"DIP2C"': 9.519107538117833e-05, '"DRAP1"': 9.533072659306056e-05, '"PNPLA3"': 9.537506598842957e-05, '"GNAS"': 9.549469659576559e-05, '"EPS8L2"': 9.785234234179494e-05, '"GEN1"': 9.854326631327114e-05, '"CDK2AP2"': 9.897910424101781e-05, '"AP1S3"': 9.946327224838155e-05, '"ARHGEF26"': 9.988335518334424e-05, '"ZNF317"': 0.0001003678657856253, '"RNF215"': 0.00010040176185357642, '"ZBTB2"': 0.0001006425024156871, '"RAD54L2"': 0.00010139075859807184, '"PRR34-AS1"': 0.00010270907350390408, '"C16orf95-DT"': 0.00010329651656062649, '"IFI27L2"': 0.00010335290004919785, '"ZNF318"': 0.00010387724239624412, '"MTND1P23"': 0.00010413790521401813, '"THRB"': 0.00010437719178803204, '"GADD45A"': 0.00010441843012304894, '"LAMA5"': 0.00010448966196152971, '"RP9"': 0.00010462512019264914, '"CAPG"': 0.00010467188362033202, '"BRI3"': 0.0001050461275545114, '"FZD8"': 0.00010514314587448336, '"GNG5"': 0.00010544027129291479, '"ZDHHC12"': 0.00010614621519188457, '"H19"': 0.00010671360547595095, '"RNF187"': 0.00010692729700516039, '"MAD2L1"': 0.00010693777681733357, '"LINC02484"': 0.00010735008612004811, '"RNF170"': 0.00010740941753471206, '"NARF"': 0.00010792631277504738, '"MTUS1"': 0.00010800188495411266, '"REST"': 0.00010813817306530907, '"C3orf14"': 0.00010837221610347729, '"FBXO48"': 0.00010949929642405008, '"HRAS"': 0.00010962081785610867, '"PLEKHG3"': 0.00010981557525246879, '"CLIP2"': 0.0001098775902225552, '"ZCCHC3"': 0.0001099889957199951, '"ARID3A"': 0.00011049910756245505, '"SNRPA"': 0.00011083798689737334, '"HSBP1L1"': 0.00011085081070646822, '"MED25"': 0.00011087960224140463, '"SPRYD3"': 0.00011230633004227786, '"LGALS1"': 0.00011252962213845822, '"ST14"': 0.00011261287661263093, '"NTAN1"': 0.00011274401708269495, '"MPDU1"': 0.000113112189889286, '"RETREG2"': 0.00011314890103817645, '"IER3IP1"': 0.00011325837021083573, '"EFNA5"': 0.00011327538044139139, '"GFOD1"': 0.00011346673226563618, '"SMIM10L1"': 0.0001135831479855334, '"OVCH1-AS1"': 0.00011359786551073936, '"ZNF703"': 0.00011390678356827247, '"ZDHHC4"': 0.00011422613461722407, '"LETM1"': 0.00011433749070673951, '"ATP5MC2"': 0.00011443131422469909, '"LINC01186"': 0.00011451270473605318, '"GHDC"': 0.00011466050736524017, '"PKP4"': 0.00011470211687179292, '"CCDC167"': 0.00011530559316571126, '"GAS6-DT"': 0.00011566112644799607, '"AK4"': 0.00011578126010488499, '"TUBA5P"': 0.00011579587111841948, '"HIGD1A"': 0.00011603144918974072, '"PRR14L"': 0.00011613470364199224, '"METTL5"': 0.00011625366907778021, '"ARMC5"': 0.00011657601017039747, '"FBXO38"': 0.00011675847765401978, '"TRIM35"': 0.0001168588221742331, '"DLG5"': 0.00011696086656731437, '"MOCOS"': 0.00011712011847751899, '"AK1"': 0.0001172001200381172, '"BDH2"': 0.00011731152727378876, '"MAP2"': 0.00011759969220945005, '"SNCG"': 0.00011806264171637302, '"SYNJ2"': 0.00011821252883104283, '"TAF13"': 0.00011831106736291184, '"MAP3K1"': 0.00011857786180624894, '"KLC2"': 0.00011878963253162813, '"PIH1D2"': 0.00011902823945175968, '"CASP6"': 0.00011926328241788483, '"TNFRSF12A"': 0.00011933424494054425, '"DNPH1"': 0.00011942821694430839, '"SRI"': 0.00011951080167769256, '"NIF3L1"': 0.0001195563151145438, '"WNT4"': 0.00011969610963587537, '"TAF10"': 0.00011973291807516789, '"PPP2R1A"': 0.00012006915911628127, '"HNRNPUL2"': 0.00012037412729576339, '"TMEM80"': 0.00012043212378524098, '"TMEM52"': 0.00012048331810583885, '"PRPSAP2"': 0.00012056504461452058, '"SGSM2"': 0.00012064941414403926, '"DNAJB2"': 0.00012075885175690466, '"RBFOX2"': 0.00012080630682677676, '"CCDC168"': 0.00012083020629425094, '"DNMT3A"': 0.0001208411670541617, '"PKD1L1"': 0.00012086419313913725, '"RBX1"': 0.00012110749400077944, '"HEY2"': 0.00012113206549610044, '"NAXD"': 0.00012118143245078909, '"TIMP3"': 0.00012127401791918428, '"PGLS"': 0.00012132219355948139, '"DOP1A"': 0.00012139536228254638, '"SIGMAR1"': 0.00012159502584419396, '"BMPR1B"': 0.00012160986674253551, '"WDR77"': 0.00012169362002452024, '"H2AX"': 0.00012174716463181668, '"MMP2"': 0.00012180600844963568, '"POLDIP2"': 0.00012180896215430489, '"ATN1"': 0.00012182387847957645, '"SAP30-DT"': 0.00012195692598539647, '"DTD1"': 0.00012201293947961133, '"CRYZL1"': 0.00012201525125862446, '"PSG2"': 0.0001221944594087437, '"LIMS1"': 0.0001223283842012364, '"RSPH3"': 0.00012243236084508998, '"CPE"': 0.0001227372056490503, '"RPA1"': 0.00012287760762013828, '"HDDC3"': 0.00012302841142860176, '"SMAD3"': 0.0001230618451068284, '"HMG20B"': 0.000123268499797269, '"SLC30A6-DT"': 0.00012349671014544978, '"ZNF710"': 0.00012358647021590182, '"KCNG1"': 0.00012372234995197817, '"XPNPEP1"': 0.00012375380541634418, '"CMTM3"': 0.00012388457106531097, '"XRCC1"': 0.00012389818029954659, '"MTCO1P12"': 0.0001239066255511715, '"CNPY2-AS1"': 0.000123978013359157, '"ZFP3"': 0.00012425801112360326, '"EIF3J-DT"': 0.0001242738966972122, '"SYK"': 0.0001243584342056804, '"WDR82"': 0.00012478520999293445, '"DEPDC1B"': 0.0001248311720088767, '"SECISBP2"': 0.00012502114117801338, '"RPL22L1"': 0.00012584043289891474, '"TRMT5"': 0.00012631556550004463, '"SNX18"': 0.0001266687430191914, '"ADM"': 0.0001272428638717744, '"TBC1D16"': 0.00012732167287889777, '"TMEM52B"': 0.00012781592178763432, '"LSM4"': 0.00012806581544119736, '"FLOT1"': 0.00012876617843898846, '"MGMT"': 0.0001289780742360211, '"CIRBP"': 0.0001293075716925879, '"CSTA"': 0.00012968801141404157, '"CBX4"': 0.00013007665825703584, '"LINC01503"': 0.00013109535665441384, '"CRBN"': 0.0001316174349324653, '"FAM20C"': 0.00013178421636747436, '"MRFAP1"': 0.00013181071769579965, '"CUL4B"': 0.00013188720328651335, '"SLC6A8"': 0.00013272122297906968, '"LARP7"': 0.00013279544580742015, '"SINHCAFP3"': 0.0001328044859655438, '"SLC1A5"': 0.00013280640609334722, '"LEO1"': 0.00013369965894821154, '"RGPD4-AS1"': 0.00013373196245833238, '"EIF5AL1"': 0.00013388410844752068, '"ERI1"': 0.00013406997792322223, '"NUAK1"': 0.0001347850111246652, '"NT5C"': 0.00013491372407668716, '"SPINT1-AS1"': 0.00013591083365971222, '"MCM6"': 0.00013699387077204835, '"MAST4"': 0.0001375255393880784, '"EPPK1"': 0.00013755273657208256, '"LRAT"': 0.0001378065417063106, '"UQCRHL"': 0.00013824814226107797, '"PPARA"': 0.0001383822420858464, '"MACROH2A2"': 0.00013843042672545986, '"FGF12"': 0.00013849370413761874, '"FARS2"': 0.00013874042621543696, '"TOLLIP"': 0.0001387481264159155, '"TCF19"': 0.0001387526894875243, '"PMVK"': 0.00013892533844142463, '"SFMBT1"': 0.00013939926774223904, '"EPB41L1"': 0.00013964520791177152, '"ENTR1"': 0.00013970504058774652, '"MLLT6"': 0.00013977625484825124, '"MAP7"': 0.00013977896300606187, '"BCL2L12"': 0.0001398891350738934, '"ZNF358"': 0.000139997291988734, '"AGK"': 0.00014018992292080915, '"KIF16B"': 0.00014021658110190932, '"YTHDF1"': 0.00014039134346719367, '"RAB31"': 0.00014066593303094224, '"ZNF341"': 0.00014089099181445317, '"NSMF"': 0.00014107067480810079, '"EPB41L2"': 0.00014116957814905927, '"ZBTB45"': 0.00014172908276723547, '"SMDT1"': 0.00014204998914664227, '"BICD1"': 0.00014211257706998222, '"CHCHD7"': 0.00014223689746741339, '"PALM3"': 0.00014232724239321431, '"FRY"': 0.0001424879096884028, '"RAB2B"': 0.00014280249016388093, '"FANCE"': 0.0001428659480758485, '"FBXL17"': 0.00014298120261336877, '"POLR3A"': 0.000143064757670291, '"NUDT14"': 0.00014319795518086064, '"ZBTB38"': 0.0001432257079387805, '"UGT1A7"': 0.0001434009624943753, '"SLC25A28"': 0.0001435953485596018, '"COL6A3"': 0.00014365185016641896, '"SPRYD4"': 0.00014379284498794594, '"WHAMMP3"': 0.00014427154512712735, '"TCEAL9"': 0.00014494015369892848, '"IPMK"': 0.0001450290991585605, '"BTBD7P1"': 0.000145134472644446, '"LINC01666"': 0.00014526646640719654, '"CDC42BPA"': 0.0001454489489095823, '"DGUOK-AS1"': 0.0001454845037696547, '"RGL2"': 0.00014596042815469962, '"MED18"': 0.00014646207518966155, '"PCBD1"': 0.00014669492695102294, '"TCF20"': 0.00014669718896807095, '"HIVEP3"': 0.00014671497421901727, '"HOXC13-AS"': 0.0001469121023727771, '"TMEM238"': 0.00014721665603321108, '"CDC42EP1"': 0.0001473009747659587, '"FOXN3-AS1"': 0.00014747924933003224, '"IGFBP7"': 0.00014781069821093247, '"EEF1A2"': 0.000147831919833748, '"NACA4P"': 0.00014797309164687247, '"COX8A"': 0.00014817704510606476, '"PRR15"': 0.00014827297878121777, '"MSANTD3"': 0.0001490383761172522, '"CACTIN"': 0.0001491334435922437, '"GPRC5D-AS1"': 0.00014930632015493645, '"MZT1"': 0.0001502919297752565, '"UACA"': 0.00015086844717421142, '"CYB561D1"': 0.00015088608314831162, '"SETD1A"': 0.00015116568407417562, '"GNL1"': 0.00015134480612421635, '"RHPN1"': 0.00015140470719763807, '"SRP14-DT"': 0.00015148825016325797, '"MON1B"': 0.00015150735457115791, '"KDM4B"': 0.0001516624763269218, '"PCYT1B"': 0.00015208738348943627, '"KXD1"': 0.00015226379131071647, '"CUL9"': 0.00015236603617199636, '"ROCK2"': 0.00015252522572891896, '"IL17RC"': 0.00015264395447948915, '"DCAF10"': 0.00015272574419645073, '"DDX23"': 0.00015289283858510542, '"ZADH2"': 0.00015324261243444056, '"TDO2"': 0.00015356742662741272, '"WDR18"': 0.00015373856397547713, '"SDHAF3"': 0.00015445037858791084, '"LINC02762"': 0.00015458299560744217, '"GPT2"': 0.00015459434870704076, '"ZXDC"': 0.0001547525424039918, '"TCHH"': 0.00015497189106256963, '"FLNC"': 0.00015533566568557664, '"COL7A1"': 0.00015586506112036635, '"PDLIM1"': 0.00015633405505658857, '"MAP3K4"': 0.00015668437391769754, '"CDK2AP1"': 0.0001567696040824092, '"RGS10"': 0.0001582471327704298, '"RPLP0P2"': 0.00015831099771027778, '"UBP1"': 0.00015900489847027704, '"PAPSS1"': 0.00015910059433376514, '"PHEX"': 0.0001596523651005432, '"EPB41L4B"': 0.00015968706183195608, '"SUPT3H"': 0.00015985688081170197, '"UBE2Q2"': 0.00015993547411619218, '"TMPRSS13"': 0.00015997746965016498, '"ANKRA2"': 0.0001605402364055497, '"JUP"': 0.0001607065553736623, '"PAQR8"': 0.00016087969941596978, '"SLC35C2"': 0.0001612077375290849, '"RB1CC1"': 0.00016123124114455033, '"CAMK2N1"': 0.00016133172529245236, '"SDC1"': 0.0001614349726221707, '"RHOT2"': 0.0001615036347989111, '"ZNF33B"': 0.00016284795410101034, '"SMARCC1"': 0.0001630753212198574, '"TEAD3"': 0.00016310439753014247, '"SEMA3D"': 0.00016442494989453823, '"MT-ND6"': 0.00016488432553469316, '"CCDC50"': 0.00016562555626894727, '"MYBL1"': 0.0001662333539466515, '"MTA2"': 0.00016682192232410277, '"KLF6"': 0.00016734128566464108, '"NCLN"': 0.00016739315947304791, '"PPIH"': 0.00016754462102097964, '"NCOR1"': 0.00016828011239194022, '"MED29"': 0.0001687805017255413, '"DCAKD"': 0.0001693125874126384, '"ARMC6"': 0.0001694209914248084, '"MBD6"': 0.00017098245419201882, '"ATP2A2"': 0.00017163996850738295, '"PRR5L"': 0.00017269059028718567, '"DECR2"': 0.00017384673708112087, '"MIR4458HG"': 0.00017478570323205695, '"ZNF469"': 0.00017537467178658115, '"RNF4"': 0.00017595495500738093, '"H3-3A"': 0.00017650648642081332, '"METRN"': 0.00017699488147204253, '"DGKZ"': 0.0001771227169278293, '"SCRIB"': 0.00017739087023958553, '"FAM81A"': 0.00017780192052760857, '"PLK1"': 0.00017797691054821755, '"BRCC3"': 0.00017810310511273713, '"PALLD"': 0.0001784995719674682, '"UBC"': 0.0001786011197531431, '"SYT14"': 0.00017864504268805893, '"USP53"': 0.00017912369420959083, '"HOXB7"': 0.00018056481352029337, '"SYNPO2L"': 0.00018081050597185252, '"LINC01133"': 0.00018097968389972808, '"PUSL1"': 0.00018143993905509644, '"SS18"': 0.00018154864505853552, '"FAM166A"': 0.00018161522952676656, '"C12orf60"': 0.00018171760625134743, '"DAZAP2"': 0.00018194137349465645, '"SLC2A4RG"': 0.00018202418736450868, '"NDUFC1"': 0.0001821372164412965, '"MID1"': 0.00018336929968838504, '"LINC02225"': 0.00018444397776482937, '"MT-ND3"': 0.00018503905775842504, '"SRA1"': 0.00018529082468693082, '"GADD45B"': 0.0001853003540953347, '"ZNF581"': 0.00018593024811010094, '"LINC02018"': 0.00018593571083524863, '"ZFYVE9"': 0.00018620848833776505, '"KEAP1"': 0.00018750375227549808, '"LINC02428"': 0.00018930031329613702, '"NUDT1"': 0.00018932778893486116, '"PAIP2"': 0.00018947410963233118, '"AXL"': 0.00018971864173324333, '"INO80E"': 0.0001898314778185876, '"CARMIL1"': 0.00019004697446569225, '"KAT7"': 0.0001902726439852345, '"TCEAL4"': 0.00019064747185285202, '"ERO1A"': 0.00019090428118907903, '"PIN4"': 0.00019219633773639495, '"C1QL1"': 0.00019224643293327316, '"EHD2"': 0.00019340659009420633, '"SCAF8"': 0.00019455678517928175, '"MARK1"': 0.0001947587678334637, '"ARHGEF10L"': 0.00019663098855457733, '"PSIP1"': 0.0001988955083314893, '"BIN1"': 0.00019946062278649156, '"CFD"': 0.00019982069174368555, '"UBE2E1"': 0.0002009432879025122, '"SRSF8"': 0.0002013268579142839, '"PAQR7"': 0.00020242481631119582, '"PRR11"': 0.00020264262383601185, '"LHPP"': 0.00020393429470550364, '"HDAC7"': 0.0002041592020323898, '"FPGS"': 0.0002044836497266115, '"MACC1"': 0.0002045851977443068, 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0.00021775543250839133, '"CELSR1"': 0.00021786590724382545, '"GIN1"': 0.0002188835486894249, '"YKT6"': 0.00021951594622034295, '"NEK2"': 0.00021979335492632786, '"NMD3"': 0.0002203244375751095, '"SOS1"': 0.00022059732799120424, '"JUN"': 0.00022067201360735002, '"MAP3K14"': 0.00022074583775865764, '"RPL7A"': 0.00022081364688267282, '"UBN2"': 0.00022205029148486666, '"TAF12"': 0.00022235481489265907, '"PPL"': 0.00022280824260630555, '"STT3A"': 0.00022422654083296034, '"DANT1"': 0.00022638805188288837, '"EFNB2"': 0.00022728547652785288, '"VPS54"': 0.00022800701572882518, '"ARSA"': 0.00022831864782816118, '"RNF122"': 0.00022889370076248881, '"CTBP2"': 0.00022979510135933543, '"PTPRE"': 0.00023028928716584815, '"POLR2J"': 0.00023076377020489952, '"SKI"': 0.00023179418181368963, '"PLEKHA7"': 0.0002318493984716956, '"POLR2F"': 0.0002323835170403406, '"CFAP36"': 0.00023244554674763243, '"PHF3"': 0.00023253408993065267, '"BOD1L1"': 0.00023327769179906817, '"SCP2"': 0.00023329208702506637, 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0.00043530788975727183, '"ATP1A1"': 0.00043543306819751636, '"HCFC1"': 0.00043937438837525386, '"SPRR1B"': 0.0004418578340316488, '"TTC19"': 0.00045061485020778894, '"APLP2"': 0.00045087891198505013, '"OAZ1"': 0.0004532228008441457, '"BTN3A2"': 0.00045452858638629184, '"HDGF"': 0.0004552017480606947, '"UTP3"': 0.00045591377925683214, '"PKM"': 0.0004582663413994382, '"FOXP1"': 0.0004583338939235477, '"YTHDC1"': 0.0004596165412689891, '"PRRC2A"': 0.0004620988233756909, '"DDX54"': 0.00046506020400071844, '"MRPL33"': 0.00046557188716919744, '"FUBP3"': 0.0004670429393451198, '"TMEM141"': 0.0004689799961638787, '"C19orf53"': 0.0004758452390637677, '"POLR2A"': 0.00047769979941288164, '"ZHX1"': 0.00047917768851362004, '"NDUFB1"': 0.0004810422004718799, '"FAM120A"': 0.00048459548494541037, '"MKI67"': 0.0004864480080550832, '"KIAA1522"': 0.0004867363448646368, '"CAVIN1"': 0.0004882713077240299, '"SHOX"': 0.0004917225983215569, '"PRRG3"': 0.0004934679595819938, '"SNHG9"': 0.0004945823833645541, '"RPL18A"': 0.0004955480378029153, '"RPS6KA6"': 0.0004957658264686902, '"HMGN3"': 0.0004973207434192626, '"SLC25A53"': 0.0005020867463688065, '"LBH"': 0.0005040528782945797, '"MT-CO3"': 0.0005249976432624325, '"TSR1"': 0.0005305574740182297, '"S100A2"': 0.0005337622122217089, '"ZBTB33"': 0.0005349652600099973, '"STRN4"': 0.0005456492112037108, '"FLNA"': 0.0005462958889448675, '"MZT2B"': 0.0005474191500048607, '"RRS1"': 0.0005484191019273374, '"ATOX1"': 0.0005494395131447357, '"GUK1"': 0.0005514852555694694, '"PLBD2"': 0.0005573665474277789, '"MT-CO2"': 0.000564378438966458, '"HMGA1"': 0.0005681849058004241, '"RAB4A"': 0.0005686202364119833, '"FGFR1OP2"': 0.0005700015830417413, '"TOP2A"': 0.0005718345157763944, '"SNRNP70"': 0.0005743624195706353, '"RBM23"': 0.0005844451475604752, '"MRPL55"': 0.0005847441746237499, '"CBX3"': 0.0005919036418648444, '"GPI"': 0.0005927958262165032, '"RPS8"': 0.0005929918522310468, '"TMA7"': 0.0005959467587331245, '"PRMT2"': 0.0005986055143350369, '"MT-ND4L"': 0.0005987771402451838, '"KRT10"': 0.0006067722931474635, '"GBP1P1"': 0.0006131868310168865, '"C4orf3"': 0.0006304991309298669, '"H1-4"': 0.000632803829471708, '"TMEM160"': 0.0006595305306552422, '"PDCD4"': 0.0006611275255486596, '"ANXA1"': 0.000665092935494461, '"PPDPF"': 0.000667262716795998, '"METTL26"': 0.0006722065897849059, '"UQCRQ"': 0.0006763182602536993, '"KRT13"': 0.0006911468454522127, '"RPL18"': 0.0006980952510066309, '"PFN1"': 0.0007009353815375238, '"ACTG1"': 0.0007080842913453339, '"SLC25A48"': 0.0007127806117647259, '"ZNF302"': 0.0007147231528305951, '"MT-ND2"': 0.0007149357749625225, '"YBX3"': 0.0007168112219539225, '"ELOB"': 0.000717755412176585, '"PDIA6"': 0.0007185432281811555, '"KDM1A"': 0.0007198692873801266, '"RPL37"': 0.0007200553039830877, '"RPSA"': 0.0007253343985169863, '"NEDD4L"': 0.0007269538533794223, '"MT-ND1"': 0.0007601737159585914, '"LIMCH1"': 0.0007729484995453888, '"NDUFB2"': 0.0007742983985061338, '"GTF3A"': 0.0007751059948149785, '"HMGB2"': 0.0007809003567787343, '"KCNJ3"': 0.0007817701081982712, '"RPS19"': 0.000783543934948658, '"CENPF"': 0.0007864922979953076, '"KIF5B"': 0.0007893887567876539, '"HSPA5"': 0.0008030834561066058, '"RTF1"': 0.000805840949478334, '"GAPDH"': 0.0008099000546113184, '"FABP5"': 0.0008191045457619936, '"CAP1"': 0.0008247117773191265, '"HSPB1"': 0.0008378221191292903, '"RPL36"': 0.0008413806930741123, '"HNRNPM"': 0.0008502139217454942, '"H1-1"': 0.0008539692925172671, '"AHNAK"': 0.0008553711742835025, '"MYH9"': 0.000855640858443516, '"RAC1"': 0.0008575683934681928, '"CCDC34"': 0.0008592509955289553, '"COPS9"': 0.0008598763456278156, '"STMN1"': 0.0008737086642316875, '"H4C5"': 0.0008795940130621462, '"TPX2"': 0.000890948270108415, '"RPS12"': 0.0008949506848809207, '"BAP1"': 0.0009048023210422446, '"PABPC1"': 0.0009066193557225819, '"MT1X"': 0.0009072928666512218, '"ZBTB20"': 0.0009128474780133695, '"H1-2"': 0.0009135586157927686, '"MT-RNR1"': 0.0009358881385485034, '"TMSB4X"': 0.0009418706316113773, '"ANP32B"': 0.0009438497352050117, '"RPS21"': 0.0009443610091810247, '"GDPGP1"': 0.0009519222329638932, '"H3C2"': 0.0009558964721222386, '"ATP5F1E"': 0.0009595705909231783, '"UQCR11"': 0.0009797563088148648, '"ATAD2"': 0.0009954073197492503, '"DSP"': 0.0009954796289557675, '"RPL13"': 0.0009988530531959234, '"RPS3"': 0.0009992763649978413, '"TPI1"': 0.0010037770005445342, '"KRT7"': 0.001025111371904589, '"EEF1A1"': 0.001035502143109066, '"LAMB3"': 0.0010941455176156183, '"GOLGA4"': 0.0011184204515008703, '"DNMT1"': 0.0011345871990638581, '"RPL35A"': 0.001138043526614551, '"PDIA3"': 0.0011427988989764011, '"HNRNPA2B1"': 0.0011433367372421274, '"S100A6"': 0.0011683803025887224, '"MIR663AHG"': 0.0011740428840993527, '"CALR"': 0.0011766494654636482, '"HEPACAM"': 0.0011808849339063172, '"RPL12"': 0.001191439778123696, '"RPS2"': 0.001194308768976981, '"TPT1"': 0.001205269850064627, '"EZR"': 0.001225071329272939, '"CAST"': 0.001225159919916652, '"RPL28"': 0.0012281776596877246, '"H1-5"': 0.0012376617979422751, '"POLR2L"': 0.0012628131438675318, '"RPL37A"': 0.0012714575125409799, '"YWHAZ"': 0.0012862580396838948, '"HNRNPU"': 0.0013231478148974817, '"H2AC11"': 0.0013281911796263423, '"GSTP1"': 0.0013413501830673359, '"RPS15"': 0.001388783900542571, '"RPL21"': 0.0014714062727704765, '"RPS14"': 0.0014894713584294318, '"H1-3"': 0.0014933048977463694, '"CACNA1A"': 0.0015069041533679968, '"CNNM2"': 0.0015486647949964705, '"AHNAK2"': 0.0015503437237867808, '"PTMS"': 0.0015628796880904309, '"SFN"': 0.0015695896986519583, '"RPL27A"': 0.001570131229194538, '"RPL10"': 0.0015934460680263676, '"MT2A"': 0.0015984518782531313, '"CAV1"': 0.001634266889971502, '"FOSL1"': 0.001751848288991023, '"EEF2"': 0.0017650241606356476, '"YBX1"': 0.0017773290857469228, '"RPL39"': 0.0018919158511813787, '"RPLP2"': 0.001919142850090759, '"SERF2"': 0.0020219946140690717, '"BTBD9"': 0.0020232340575063856, '"MARCKS"': 0.0020248640977330408, '"BNIP3L"': 0.0021710099829992512, '"PSMA7"': 0.0021931269362724707, '"MT-TQ"': 0.002193921280561021, '"NEAT1"': 0.0023997483972577976, '"CALM2"': 0.002469512531253525, '"S100A11"': 0.002591190912301445, '"RPL8"': 0.002664050357012829, '"RPS5"': 0.002678666773893195, '"NCALD"': 0.0027009453504468492, '"PLEC"': 0.0027792545992741413, '"RPLP1"': 0.0027851340383064273, '"RPL35"': 0.0029750802745726933, '"H2AC12"': 0.002995303612343034, '"MT-TV"': 0.0031023417486446153, '"P4HA1"': 0.003740750944855744, '"B4GALT1"': 0.003933912858548733, '"MT-RNR2"': 0.004101299582630042, '"ZC3H15"': 0.004387837743840847, '"FTL"': 0.004447793628914251, '"HSP90B1"': 0.004467412099537724, '"H4C3"': 0.004520148554145522, '"PGK1"': 0.00472678521672826, '"RPS27"': 0.005354758165214481, '"HSP90AB1"': 0.00596361843743688, '"KRT19"': 0.006001004129403219, '"NPM1P40"': 0.006086094091231668, '"BNIP3"': 0.006487001514071113, '"EGLN3"': 0.006493533999303821, '"ENO1"': 0.00753051878369682, '"MALAT1"': 0.007638317711998487, '"S100A10"': 0.007938665660892828, '"RPS28"': 0.009468107164498876, '"NCL"': 0.01055285492010248, '"AKR1C1"': 0.010570605898465497, '"TMSB10"': 0.011685154891367018, '"EIF3J"': 0.013421127989964313, '"HSPD1"': 0.01521398925790309, '"RPL41"': 0.018503503041994183, '"HSP90AA1"': 0.01954481606682723, '"GPM6A"': 0.02215913052583788, '"LDHA"': 0.02923350303600919, '"BCYRN1"': 0.031017949233915258, '"WDR43"': 0.03291294712318751, '"FGF23"': 0.05028077890515501, '"IGFBP3"': 0.06267123259196629, '"AKR1C2"': 0.10412354009140996, '"NDRG1"': 0.11017108099979633}

To see the differences in distribution of the gene, we plot some boxplots.

In [ ]:
Gene_Hypo = HCC1806_drop_Hypo_f_n_trans['"NDRG1"']
Gene_Hypo
Out[ ]:
"AAAAACGTCACT_Hypoxia"    1
"AAAAAGCACTTG_Hypoxia"    0
"AAAACAGCACAG_Hypoxia"    0
"AAAACCTCGGGT_Hypoxia"    0
"AAAACCTGCGCT_Hypoxia"    0
                         ..
"TTTTTACCAATC_Hypoxia"    0
"TTTTTCCGTGCA_Hypoxia"    0
"TTTTTGCCTGGG_Hypoxia"    0
"TTTTTGTAACAG_Hypoxia"    0
"TTTTTTTGAATC_Hypoxia"    0
Name: "NDRG1", Length: 8899, dtype: int64
In [ ]:
Gene_Norm = HCC1806_drop_Norm_f_n_trans['"NDRG1"']
Gene_Norm
Out[ ]:
"AAAAAACCCGGC_Normoxia"    0
"AAAACCGGATGC_Normoxia"    0
"AAAACGAGCTAG_Normoxia"    0
"AAAACTTCCCCG_Normoxia"    0
"AAAAGCCTACCC_Normoxia"    0
                          ..
"TTTTATACGAGA_Normoxia"    0
"TTTTCTTCCGAC_Normoxia"    0
"TTTTGGCGGTCA_Normoxia"    0
"TTTTGTAAGGGA_Normoxia"    0
"TTTTGTCGGGCA_Normoxia"    0
Name: "NDRG1", Length: 5783, dtype: int64
In [ ]:
Gene_Hypo.describe()
Out[ ]:
count    8899.000000
mean        0.377121
std         0.734806
min         0.000000
25%         0.000000
50%         0.000000
75%         1.000000
max         9.000000
Name: "NDRG1", dtype: float64
In [ ]:
Gene_Norm.describe()
Out[ ]:
count    5783.000000
mean        0.011932
std         0.126262
min         0.000000
25%         0.000000
50%         0.000000
75%         0.000000
max         3.000000
Name: "NDRG1", dtype: float64
In [ ]:
plt.figure(figsize=(16,16))
sns.boxplot(data=[Gene_Norm, Gene_Hypo])
plt.xticks(ticks = [0, 1], labels=["Normoxic", "Hypoxic"])
plt.title("NDRG1")
plt.show()

We can see from the plot that the gene NDRG1 has very different distribution between the hypoxic and the normoxic cells. What we can definetely see is that the outliners are very different.

Let's now plot the one we got from the first analysis.

In [ ]:
Gene_Hypo = HCC1806_drop_Hypo_f_n_trans['"IGFBP3"']
Gene_Hypo
Out[ ]:
"AAAAACGTCACT_Hypoxia"    0
"AAAAAGCACTTG_Hypoxia"    0
"AAAACAGCACAG_Hypoxia"    0
"AAAACCTCGGGT_Hypoxia"    1
"AAAACCTGCGCT_Hypoxia"    1
                         ..
"TTTTTACCAATC_Hypoxia"    0
"TTTTTCCGTGCA_Hypoxia"    0
"TTTTTGCCTGGG_Hypoxia"    0
"TTTTTGTAACAG_Hypoxia"    1
"TTTTTTTGAATC_Hypoxia"    1
Name: "IGFBP3", Length: 8899, dtype: int64
In [ ]:
Gene_Norm = HCC1806_drop_Norm_f_n_trans['"IGFBP3"']
Gene_Norm
Out[ ]:
"AAAAAACCCGGC_Normoxia"    0
"AAAACCGGATGC_Normoxia"    0
"AAAACGAGCTAG_Normoxia"    1
"AAAACTTCCCCG_Normoxia"    0
"AAAAGCCTACCC_Normoxia"    0
                          ..
"TTTTATACGAGA_Normoxia"    0
"TTTTCTTCCGAC_Normoxia"    0
"TTTTGGCGGTCA_Normoxia"    0
"TTTTGTAAGGGA_Normoxia"    0
"TTTTGTCGGGCA_Normoxia"    0
Name: "IGFBP3", Length: 5783, dtype: int64
In [ ]:
plt.figure(figsize=(16,16))

sns.boxplot(data=[Gene_Norm, Gene_Hypo])
plt.xticks(ticks = [0, 1], labels=["Normoxic", "Hypoxic"])
plt.title("IGFBP3")
plt.show()

We can see that the distribution is very different.

Clustering Data

To better visualize the data, we performed a PCA in 2 dimensions and then used the data for K-means clustering. In such a way, we are trying to split the data in two groups and, by using different colours for hypoxic and normoxic cells, check whether the clustering assigned them correctly.

In [ ]:
from sklearn.decomposition import PCA
In [ ]:
from sklearn.cluster import KMeans
In [ ]:
def plot_data_C(X, col):
  for i in range(len(X)):
    plt.plot(X[i][0], X[i][1], 'k.', markersize=2, c=col[i])

def plot_centroids_C(centroids, weights=None, circle_color='w', cross_color='k'):
    if weights is not None:
        centroids = centroids[weights > weights.max() / 10]
    plt.scatter(centroids[:, 0], centroids[:, 1],
                marker='o', s=35, linewidths=8,
                color=circle_color, zorder=10, alpha=0.9)
    plt.scatter(centroids[:, 0], centroids[:, 1],
                marker='x', s=2, linewidths=12,
                color=cross_color, zorder=11, alpha=1)

def plot_decision_boundaries(clusterer, X, col, resolution=1000, show_centroids=True,
                             show_xlabels=True, show_ylabels=True):
    mins = X.min(axis=0) - 0.1
    maxs = X.max(axis=0) + 0.1
    xx, yy = np.meshgrid(np.linspace(mins[0], maxs[0], resolution),
                         np.linspace(mins[1], maxs[1], resolution))
    Z = clusterer.predict(np.c_[xx.ravel(), yy.ravel()])
    Z = Z.reshape(xx.shape)

    plt.contourf(Z, extent=(mins[0], maxs[0], mins[1], maxs[1]),
                cmap="Pastel2")
    plt.contour(Z, extent=(mins[0], maxs[0], mins[1], maxs[1]),
                linewidths=1, colors='k')
    plot_data_C(X, col)
    if show_centroids:
        plot_centroids_C(clusterer.cluster_centers_)

    if show_xlabels:
        plt.xlabel("$x_1$", fontsize=14)
    else:
        plt.tick_params(labelbottom=False)
    if show_ylabels:
        plt.ylabel("$x_2$", fontsize=14, rotation=0)
    else:
        plt.tick_params(labelleft=False)
In [ ]:
pcaM = PCA(n_components = 2)
HCC1806_drop_lowT = pcaM.fit_transform(HCC1806_drop_f_n.T)
HCC1806_drop_ret = pcaM.inverse_transform(HCC1806_drop_lowT)
print(HCC1806_drop_lowT.shape)
(14682, 2)
In [ ]:
col = []
for c in HCC1806_drop_f_n.columns:
  if "Hypo" in c:
    col.append("r")
  else:
    col.append("b")
print(len(col))
14682
In [ ]:
index = HCC1806_drop_f_n.T.index
HCC1806_drop_hyponormo = np.zeros((len(index)), dtype = 'int64')
for i in range(len(index)):
    HCC1806_drop_hyponormo[i] = not 'Hypo' in index[i] # 0 Hypo 1 Norm
In [ ]:
from sklearn import metrics
k = 2
for i in [42, 52, 46, 37, 75]:
  kmeans = KMeans(n_clusters=k, random_state=i)
  y_pred = kmeans.fit_predict(HCC1806_drop_lowT)
  mapping = {}
  for class_id in np.unique(HCC1806_drop_hyponormo):
      mode, _ = stats.mode(y_pred[HCC1806_drop_hyponormo==class_id]) # look at all samples with a given label and study what is the most common label given by the Gaussian mixture
      mapping[mode[0]] = class_id
  y_pred = np.array([mapping[cluster_id] for cluster_id in y_pred])
  # print(accuracy_score(y_pred, MCF7_hyponormo))
  print("fraction of correct predictions", np.sum(y_pred==HCC1806_drop_hyponormo) / len(y_pred))
  plt.figure(figsize=(8, 4))
  plot_decision_boundaries(kmeans, HCC1806_drop_lowT, col)
  plt.show()
fraction of correct predictions 0.5766925486990874
fraction of correct predictions 0.5763519956409209
fraction of correct predictions 0.5764882168641874
fraction of correct predictions 0.576624438087454
fraction of correct predictions 0.5779185397084866

We tried to use different random states to calculate an average score of our K-means clustering. We can see that it predicts correctly only around 57% of the data in every case, this is probably due to the fact that a PCA in 2 dimention retain low variance in this particular dataset.

Let's now try clustering without applying PCA.

In [ ]:
from sklearn import metrics
k = 2
accuracy_scores = []
for i in [42, 52, 28, 37, 67]:
  kmeans = KMeans(n_clusters=k, random_state=i)
  y_pred = kmeans.fit_predict(HCC1806_drop_f_n.T)
  mapping = {}
  for class_id in np.unique(HCC1806_drop_hyponormo):
      mode, _ = stats.mode(y_pred[HCC1806_drop_hyponormo==class_id]) # look at all samples with a given label and study what is the most common label given by the Gaussian mixture
      mapping[mode[0]] = class_id
  y_pred = np.array([mapping[cluster_id] for cluster_id in y_pred])
  print(accuracy_score(HCC1806_drop_hyponormo, y_pred))
  print("fraction of correct predictions", np.sum(y_pred==HCC1806_drop_hyponormo) / len(y_pred))
  accuracy_scores.append(accuracy_score(HCC1806_drop_hyponormo, y_pred))
0.5875221359487808
fraction of correct predictions 0.5875221359487808
0.5872496935022476
fraction of correct predictions 0.5872496935022476
0.5875221359487808
fraction of correct predictions 0.5875221359487808
0.5875221359487808
fraction of correct predictions 0.5875221359487808
0.5870453616673478
fraction of correct predictions 0.5870453616673478
In [ ]:
print("Average accuracy score:", sum(accuracy_scores)/len(accuracy_scores))
Average accuracy score: 0.5873722926031876

We then repeated the clustering using the dataset not processed by the PCA, obtaining a slightly higher accuracy score. Even using the whole dataset, the clustering accuracy is still pretty low.

In [ ]:
from sklearn.cluster import kmeans_plusplus


k = 2
accuracy_scores = []
for i in [24, 176, 65, 98, 200]:
  centroids, indices = kmeans_plusplus(HCC1806_drop_f_n.T.to_numpy(), n_clusters = 2, random_state=i)
  kmeans = KMeans(n_clusters=k, random_state=i)
  kmeans.fit(centroids)
  y_pred = kmeans.predict(HCC1806_drop_f_n.T)
  mapping = {}
  for class_id in np.unique(HCC1806_drop_hyponormo):
      mode, _ = stats.mode(y_pred[HCC1806_drop_hyponormo==class_id]) # look at all samples with a given label and study what is the most common label given by the Gaussian mixture
      mapping[mode[0]] = class_id
  # y_pred = np.array([mapping[cluster_id] for cluster_id in y_pred])
  print(accuracy_score(HCC1806_drop_hyponormo, y_pred))
  #print("fraction of correct predictions", np.sum(y_pred==MCF7_hyponormo) / len(y_pred))
  accuracy_scores.append(accuracy_score(HCC1806_drop_hyponormo, y_pred))
print("Average accuracy score:", sum(accuracy_scores)/len(accuracy_scores))
0.564977523498161
0.6004631521591064
0.5970576215774418
0.3945647731916633
0.4794305952867457
Average accuracy score: 0.5272987331426237

We finally tried to find the centroids using K-means++ and then used them to cluster the data. We can see that the result is worse than the previous case where we used K-means.

In conclusion

To sum up, we have observed eight different datasets, four of MCF7 and four of HCC1806. Both the unfiltered data in SmartSeq were highly sparse (over 50% of zeros), and had a few duplicated rows but no null row.\ In addition, by looking at the gene expression, we observed that most of the data is contained in the outliers, and in each cell, a few genes are highly expressed.\ Both of the data sets are not normalized and overall the skewness is high for most of the cells (and never close to 0). Transformations such as PowerTransformer and QuantileTransformer didn’t work well, however applying the log_2 to the data translated by 1 reduced drastically the skewness for both cell lines.\ Then, by looking at the filtered and normalized data and by comparing gene expression between hypoxic and normoxic cells, we found that there are some genes that are particularly highly expressed in one of the two types, hence more “characteristic”. We confirmed it using random forests and then checked the accuracy of the classifications using K-means clustering. Overall, for MCF7, the differences between gene expression in normoxic and hypoxic cells were more evident, but both cell lines had similar characteristics. For HCC1806, the gene CA9 appeared to be the most important one using the log ratio method, whereas using random forests emerged PGK1. For MCF7 we obtained CYP1A1 with the log ratio and NDRG1 with the random forest. We concluded that outliers have less weight in determining hypoxic/normoxic compared to MCF7.\ Analysing the filtered and normalised data in DropSeq, we noticed that the mean of genes expressed is much lower. For MCF7, the most important gene seemed TFF1 both using the log ratio and the random forest methods. For HCC1806, IGFBP3 was the most important using the log-ratio and NDRG1 using the random forest.

We could also see how the clustering worked much better in the MCF7 SmartSeq dataset than any other.

PCA & CLUSTERING

In [ ]:
%matplotlib inline
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from sklearn.decomposition import PCA

From now on, we will use only the filtered and normalized datasets for our analysis. Starting with a PCA which maintains 95% of the variance explained, in the Smart-seq datesets, we obtain that MCF7 can be expressed by using only 20 directions while HCC1806 is expressed by using 34 directions.\ Regarding instead the Drop-seq experiment, we do not obtain very nice results, in fact, we need 162 directions for the MCF7 dataset in order to retain the 95% of the variance and 844 directions for the HCC1806. A confirmation of this comes from the fact that printing the explained variance ratio it can be seen that the variance explained is very low for the first directions.

In [ ]:
pcaM = PCA(n_components = 0.95)
MCF7_low = pcaM.fit_transform(MCF7_f_n.T)
MCF7_ret = pcaM.inverse_transform(MCF7_low)
pcaH = PCA(n_components = 0.95)
HCC1806_low= pcaH.fit_transform(HCC1806_f_n.T)
print(MCF7_low.shape, HCC1806_low.shape)
(250, 20) (182, 34)
In [ ]:
pcaMD = PCA(n_components= 0.95)
MCF7_lowd = pcaMD.fit_transform(MCF7_drop_f_n.T)
MCF7_lowd.shape
Out[ ]:
(21626, 761)
In [ ]:
pcaHD = PCA(n_components= 0.95)
HCC1806_f_n_drop_lowd = pcaHD.fit_transform(HCC1806_drop_f_n.T)
HCC1806_f_n_drop_lowd.shape
Out[ ]:
(14682, 844)
In [ ]:
# Chiedere Dropseq --- Dropseq è un dataset molto corrotto 

pcaHD.explained_variance_ratio_
Out[ ]:
array([8.42324280e-02, 6.31606719e-02, 3.88313939e-02, 2.86625432e-02,
       2.37918611e-02, 2.15674691e-02, 1.67483247e-02, 1.48044703e-02,
       1.43919415e-02, 1.25207503e-02, 1.15350858e-02, 1.14281083e-02,
       9.88305907e-03, 9.50755387e-03, 9.21652544e-03, 8.59572942e-03,
       8.06758779e-03, 7.51640737e-03, 7.28384250e-03, 7.18463401e-03,
       6.83072434e-03, 6.31045086e-03, 6.20457846e-03, 5.82192410e-03,
       5.70198427e-03, 5.61458438e-03, 5.56278485e-03, 5.47274062e-03,
       5.40164381e-03, 5.26731478e-03, 5.15247523e-03, 5.05828474e-03,
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       3.52295595e-04, 3.48856194e-04, 3.47454834e-04, 3.47006610e-04,
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       1.05677442e-04, 1.05231504e-04, 1.05088356e-04, 1.04811936e-04,
       1.04714258e-04, 1.04480817e-04, 1.04176522e-04, 1.04023642e-04,
       1.03926707e-04, 1.03715366e-04, 1.03435352e-04, 1.03266090e-04,
       1.02952083e-04, 1.02713772e-04, 1.02585634e-04, 1.02356705e-04,
       1.02142919e-04, 1.02029605e-04, 1.01717353e-04, 1.01657338e-04,
       1.01294405e-04, 1.00993043e-04, 1.00949526e-04, 1.00669040e-04,
       1.00263690e-04, 1.00118814e-04, 1.00009118e-04, 9.99203130e-05,
       9.96354270e-05, 9.94810657e-05, 9.93236695e-05, 9.90831553e-05,
       9.88324031e-05, 9.87817748e-05, 9.85150632e-05, 9.81974262e-05,
       9.80483613e-05, 9.79732616e-05, 9.77062937e-05, 9.75626982e-05,
       9.74902522e-05, 9.72461322e-05, 9.71671682e-05, 9.70271889e-05,
       9.68380384e-05, 9.65652990e-05, 9.64589286e-05, 9.62099610e-05,
       9.60390973e-05, 9.59641368e-05, 9.57222629e-05, 9.56768220e-05,
       9.53012285e-05, 9.51323670e-05, 9.49690570e-05, 9.48404689e-05,
       9.47816308e-05, 9.45092039e-05, 9.43887170e-05, 9.41866356e-05,
       9.38551502e-05, 9.37171815e-05, 9.36448992e-05, 9.33497119e-05,
       9.32016506e-05, 9.30671549e-05, 9.29235742e-05, 9.27810874e-05,
       9.26922562e-05, 9.23654020e-05, 9.22354199e-05, 9.20937593e-05,
       9.18652041e-05, 9.18395245e-05, 9.16011371e-05, 9.14067594e-05,
       9.13277051e-05, 9.11014082e-05, 9.09470864e-05, 9.08747215e-05,
       9.07881329e-05, 9.05191473e-05, 9.04262530e-05, 9.03169459e-05,
       9.01501461e-05, 8.99729116e-05, 8.98473944e-05, 8.95489902e-05,
       8.94577281e-05, 8.92720625e-05, 8.91324257e-05, 8.90043338e-05,
       8.87746021e-05, 8.86660010e-05, 8.83907540e-05, 8.82592564e-05,
       8.81128488e-05, 8.78672946e-05, 8.76910862e-05, 8.75492437e-05])

To facilitate the following analysis we create an np.array that stores a binary value for each cell of the dataset: 0 if the cell is Hypo and 1 if it is Norm.

In [ ]:
# MCF7 SmartSeq

index = MCF7_f_n.T.index
MCF7_hyponormo = np.zeros((len(index)), dtype = 'int64')
for i in range(len(index)):
    MCF7_hyponormo[i] = not 'Hypo' in index[i] # 0 Hypo 1 Norm
In [ ]:
# HCC SmartSeq

index = HCC1806_f_n.T.index
HCC1806_hyponormo = np.zeros((len(index)), dtype = 'int64')
for i in range(len(index)):
    HCC1806_hyponormo[i] = not 'Hypo' in index[i] # 0 Hypo 1 Norm
In [ ]:
# MCF7 DropSeq

index = MCF7_drop_f_n.T.index
MCF7_hyponorm = np.zeros((len(index)), dtype = 'int64')
for i in range(len(index)):
    MCF7_hyponorm[i] = not 'Hypo' in index[i] # 0 Hypo 1 Norm
print(MCF7_hyponorm.size)
21626
In [ ]:
# HCC DropSeq

index = HCC1806_drop_f_n.T.index
HCC1806_hyponorm = np.zeros((len(index)), dtype = 'int64')
for i in range(len(index)):
    HCC1806_hyponorm[i] = not 'Hypo' in index[i] # 0 Hypo 1 Norm

PCA

In [ ]:
cumsum = np.cumsum(pcaM.explained_variance_ratio_)
d = np.argmax(cumsum >= 0.95) + 1
d
Out[ ]:
20

Now, we plot the explained variance ratio for the MCF7 dataset (Smartseq) and it emerges quite evidently that using the first twenty directions the explained variance ratio is almost saturated.

In [ ]:
plt.figure(figsize=(6,4))
plt.plot(cumsum, linewidth=3)
plt.axis([0, 50, 0, 1])
plt.xlabel("Dimensions")
plt.ylabel("Explained Variance")
plt.title("MCF7 SmartSeq")
plt.plot([d, d], [0, 0.95], "k:")
plt.plot([0, d], [0.95, 0.95], "k:")
plt.plot(d, 0.95, "ko")
plt.annotate("Elbow", xy=(65, 0.85), xytext=(70, 0.7),
             arrowprops=dict(arrowstyle="->"), fontsize=16)
plt.grid(True)
# save_fig("explained_variance_plot")
plt.show()

HCC1806 SQ

In [ ]:
cumsum = np.cumsum(pcaH.explained_variance_ratio_)
d = np.argmax(cumsum >= 0.95) + 1
d
Out[ ]:
34

Now, we plot the explained variance ratio for the HCC1806 dataset (Smartseq) and it emerges quite evidently that using the first twenty directions the explained variance ratio is almost saturated.

In [ ]:
plt.figure(figsize=(6,4))
plt.plot(cumsum, linewidth=3)
plt.axis([0, 50, 0, 1])
plt.xlabel("Dimensions")
plt.ylabel("Explained Variance")
plt.title("HCC1806 SmartSeq")
plt.plot([d, d], [0, 0.95], "k:")
plt.plot([0, d], [0.95, 0.95], "k:")
plt.plot(d, 0.95, "ko")
plt.annotate("Elbow", xy=(65, 0.85), xytext=(70, 0.7),
             arrowprops=dict(arrowstyle="->"), fontsize=16)
plt.grid(True)
# save_fig("explained_variance_plot")
plt.show()

MCF7 DQ

In [ ]:
cumsum = np.cumsum(pcaMD.explained_variance_ratio_)
d = np.argmax(cumsum >= 0.95) + 1
d
Out[ ]:
761

Now, we plot the explained variance ratio for the MCF7 dataset (DropSeq) and it emerges quite evidently that using the first twenty directions the explained variance ratio is almost saturated.

In [ ]:
plt.figure(figsize=(6,4))
plt.plot(cumsum, linewidth=3)
plt.axis([0, 1000, 0, 1])
plt.xlabel("Dimensions")
plt.ylabel("Explained Variance")
plt.title("MCF7 DropSeq")
plt.plot([d, d], [0, 0.95], "k:")
plt.plot([0, d], [0.95, 0.95], "k:")
plt.plot(d, 0.95, "ko")
# plt.annotate("Elbow", xy=(65, 0.85), xytext=(70, 0.7), arrowprops=dict(arrowstyle="->"), fontsize=16)
plt.grid(True)
# save_fig("explained_variance_plot")
plt.show()

HCC1806 DQ

In [ ]:
cumsum = np.cumsum(pcaHD.explained_variance_ratio_)
d = np.argmax(cumsum >= 0.95) + 1
d
Out[ ]:
844

Now, we plot the explained variance ratio for the HCC1806 dataset (DropSeq) and it emerges quite evidently that using the first twenty directions the explained variance ratio is almost saturated.

In [ ]:
plt.figure(figsize=(6,4))
plt.plot(cumsum, linewidth=3)
plt.axis([0, 1000, 0, 1])
plt.xlabel("Dimensions")
plt.ylabel("Explained Variance")
plt.title("HCC1806 DropSeq")
plt.plot([d, d], [0, 0.95], "k:")
plt.plot([0, d], [0.95, 0.95], "k:")
plt.plot(d, 0.95, "ko")
# plt.annotate("Elbow", xy=(65, 0.85), xytext=(70, 0.7), arrowprops=dict(arrowstyle="->"), fontsize=16)
plt.grid(True)
# save_fig("explained_variance_plot")
plt.show()

Plotting in 3 dimensions

Plotting the PCA results using the first three dimensions, for the SmartSeq experiment we can actually start to see that hypoxia and normoxia cells could be clustered, with the exception of some outliers. On the contrary, this is less evident with the plotting of the DropSeq experiment.

In [ ]:
MCF7_colors = []
for c in MCF7_hyponormo:
  if c == 1:
    MCF7_colors.append("r")
  else:
    MCF7_colors.append("b")
print(len(MCF7_colors))
250
In [ ]:
# MCF7_low SmartSeq

ax = plt.axes(projection='3d')
ax.scatter3D(MCF7_low[:, 0], MCF7_low[:, 1], MCF7_low[:, 2], c=MCF7_colors)

plt.title("Red are normoxic, blue are hypoxic")
plt.show()
In [ ]:
HCC1806_colors = []
for c in HCC1806_hyponormo:
  if c == 1:
    HCC1806_colors.append("r")
  else:
    HCC1806_colors.append("b")
print(len(HCC1806_colors))
182
In [ ]:
# HCC1806_low SmartSeq
%matplotlib inline

ax = plt.axes(projection='3d')
ax.scatter3D(HCC1806_low[:, 0], HCC1806_low[:, 1], HCC1806_low[:, 2], c=HCC1806_colors)
plt.title("Red are normoxic, blue are hypoxic")
plt.show()
In [ ]:
MCF7d_colors = []
for c in MCF7_hyponorm:
  if c == 1:
    MCF7d_colors.append("r")
  else:
    MCF7d_colors.append("b")
print(len(MCF7d_colors))
21626
In [ ]:
# MCF7_lowd (Dropseq)
%matplotlib inline

ax = plt.axes(projection='3d')
ax.scatter3D(MCF7_lowd[:, 0], MCF7_lowd[:, 1], MCF7_lowd[:, 2], c=MCF7d_colors, s=0.5, edgecolor=(0,0,0,0))

#ax.view_init(120, 120)

plt.title("Red are normoxic, blue are hypoxic")
plt.show()
In [ ]:
HCC1806d_colors = []
for c in HCC1806_hyponorm:
  if c == 1:
    HCC1806d_colors.append("r")
  else:
    HCC1806d_colors.append("b")
print(len(HCC1806d_colors))
14682
In [ ]:
# HCC1806_f_n_drop_lowd (DropSeq)

ax = plt.axes(projection='3d')
ax.scatter3D(HCC1806_f_n_drop_lowd[:, 0], HCC1806_f_n_drop_lowd[:, 1], HCC1806_f_n_drop_lowd[:, 2], c=HCC1806d_colors, edgecolors=(0,0,0,0))
plt.title("Red are normoxic, blue are hypoxic")
plt.show()
In [ ]:
from sklearn.cluster import KMeans, AgglomerativeClustering
from scipy.cluster.hierarchy import dendrogram
k = 2
kmeans = KMeans(n_clusters=4, random_state=42)
y_pred = kmeans.fit_predict(MCF7_f_n.T)
#np.argwhere(y_pred != 0)

GAUSSIAN MIXTURE

We decided to perform Gaussian Model Mixture, in order to see if an unsupervised learning model, based on the probability of different gaussian distribution, (in this case 2), would have found indipendently the two clusters we are dealing with: normoxia and hypoxia state of cells.

MCF7 on 3D datas

In [ ]:
MCF7_3D = np.array([MCF7_low[:, 0], MCF7_low[:, 1], MCF7_low[:, 2]])
In [ ]:
gm = GaussianMixture(n_components=2, random_state=42).fit(MCF7_3D.T)
y_pred = gm.predict(MCF7_3D.T)
y_pred
Out[ ]:
array([0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0,
       0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0,
       0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0,
       0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0,
       0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1,
       0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0,
       0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0,
       0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0,
       0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0,
       0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0,
       0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 1, 0, 0, 1, 1, 1, 1, 1, 1,
       0, 0, 0, 1, 1, 1, 1, 1])
In [ ]:
mapping = {}
for class_id in np.unique(MCF7_hyponormo):
    mode, _ = stats.mode(y_pred[MCF7_hyponormo==class_id]) # look at all samples with a given label and study what is the most common label given by the Gaussian mixture
    print(stats.mode(y_pred[MCF7_hyponormo ==class_id]))
    mapping[mode[0]] = class_id
mapping
ModeResult(mode=array([1]), count=array([124]))
ModeResult(mode=array([0]), count=array([121]))
Out[ ]:
{0: 1, 1: 0}
In [ ]:
y_pred = np.array([mapping[cluster_id] for cluster_id in y_pred])
y_pred
Out[ ]:
array([1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1,
       1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1,
       1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1,
       1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1,
       1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0,
       1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1,
       1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1,
       1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1,
       1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1,
       1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1,
       1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0,
       1, 1, 1, 0, 0, 0, 0, 0])
In [ ]:
print("correct predictions: ", np.sum(y_pred==MCF7_hyponormo))
print("fraction of correct predictions", np.sum(y_pred==MCF7_hyponormo) / len(y_pred))

array_errors = []
for i, j, k in zip( y_pred, MCF7_hyponormo, range(len(y_pred))):
    if i!=j:
        array_errors.append(MCF7_3D[:,k])
len(array_errors)
correct predictions:  245
fraction of correct predictions 0.98
Out[ ]:
5
In [ ]:
ax = plt.axes(projection='3d')
plt.figure(figsize=(50,50))
ax.scatter3D(MCF7_3D[0], MCF7_3D[1], MCF7_3D[2], c=MCF7_colors) 
ax.scatter3D(array_errors[0], array_errors[1],  c= "r")
ax.set_title("Red are normoxic, blue are hypoxic")
plt.show()
<Figure size 3600x3600 with 0 Axes>

For the only purpose to have a nice plot, we applied GMM on the dataset constituted by the first 3 dimensions of PCA ran on the MCF7 f normalized and smartseq. (Notice that, we did so since we previously commented and observed that in this case the first 3 dimensions explain a lot of the variance).

For the sake of clarity and better understanding on the problem, by looking at the graph we can see that the two states are enoughly divided in two gaussian bubbles, of course relative to the translation in this subspace we performed.

We highlighted in red the missclassified cells, later on in the classificator we will take them in special consideration, to double check if our classificator will perform better than this GMM distinction.

As we can see GMM perform a distinction betweeen normoxia and hypoxia pretty accurate: 98% of the predictions are correct and only 5 cells in total are misclassified. This could be due to numerical problems of GMM or either by lab problems. In fact we should keep in mind that while performing the sequentiation some cells could change state (from normoxia to hypoxia) based on environment state (i. e. cells put at the margin during the sequentiation.

MCF7 on whole dataset

In [ ]:
gm_whole = GaussianMixture(n_components=2, random_state=42, reg_covar=1e-5).fit(MCF7_f_n.T)
y_pred = gm_whole.predict(MCF7_f_n.T)
y_pred.shape
Out[ ]:
(250,)
In [ ]:
from scipy import stats

mapping = {}
for class_id in np.unique(MCF7_hyponormo):
    mode, _ = stats.mode(y_pred[MCF7_hyponormo==class_id]) # look at all samples with a given label and study what is the most common label given by the Gaussian mixture
    print(stats.mode(y_pred[MCF7_hyponormo ==class_id]))
    mapping[mode[0]] = class_id
mapping
ModeResult(mode=array([1]), count=array([116]))
ModeResult(mode=array([0]), count=array([126]))
Out[ ]:
{0: 1, 1: 0}
In [ ]:
y_pred = np.array([mapping[cluster_id] for cluster_id in y_pred])
y_pred
Out[ ]:
array([1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1,
       1, 0, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 0, 1, 1, 1, 1,
       1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1,
       1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 1, 1,
       1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0,
       1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1,
       1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 1, 1, 1,
       1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1,
       1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 0, 1, 1, 1,
       1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1,
       1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0,
       1, 1, 1, 1, 1, 0, 0, 0])
In [ ]:
print("correct predictions: ", np.sum(y_pred==MCF7_hyponormo))
print("fraction of correct predictions", np.sum(y_pred==MCF7_hyponormo) / len(y_pred))
array_errors = []
arg_where_errors = []
for i, j, k in zip( y_pred, MCF7_hyponormo, range(len(y_pred))):
    if i!=j:
        array_errors.append(MCF7_f_n.iloc[:,k])
        arg_where_errors.append(k)
print(arg_where_errors)

position_all_errors ={}
position_all_errors["MCF7_f_n"] = arg_where_errors
correct predictions:  242
fraction of correct predictions 0.968
[26, 38, 81, 118, 127, 134, 146, 193]

Now performing GMM on the whole dataset (taking in consideration all 3000 features) we still obtain quite good results.

In this case the plot is not available, but as before we keep track of the missclassified cells to check their outcome in the classification we will build.

By checking the behaviour of the classifier we will be able to deduce if the missclassification was due to the GMM method or to a "lab problem" as explained before.

HCC1806: on whole data set

In the case of the cell line HCC1806 sequentiated trought Smart Seq technique, we will not perform GMM on the 3D data sets, because the as we already commented the PCA's first 3 dimensions didn't explained much of the variance. So in order to avoid errors due to the lack of informations given by these 3 dimensions, we will skip this part and we will proceed without a graphical insight of the problem

In [ ]:
gm = GaussianMixture(n_components=2, random_state=42).fit(HCC1806_f_n.T)
y_pred = gm.predict(HCC1806_f_n.T)
y_pred.shape
Out[ ]:
(182,)
In [ ]:
mapping = {}
for class_id in np.unique(HCC1806_hyponormo):
    mode, _ = stats.mode(y_pred[HCC1806_hyponormo==class_id]) # look at all samples with a given label and study what is the most common label given by the Gaussian mixture
    print(stats.mode(y_pred[HCC1806_hyponormo ==class_id]))
    mapping[mode[0]] = class_id
mapping
ModeResult(mode=array([1]), count=array([87]))
ModeResult(mode=array([0]), count=array([83]))
Out[ ]:
{0: 1, 1: 0}
In [ ]:
y_pred = np.array([mapping[cluster_id] for cluster_id in y_pred])
y_pred
Out[ ]:
array([1, 0, 0, 1, 0, 1, 1, 1, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 0,
       1, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 1,
       1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 1, 1, 1,
       1, 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 1,
       1, 1, 1, 1, 0, 0, 1, 0, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1,
       1, 0, 0, 1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0,
       0, 0, 1, 1, 0, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0,
       0, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0,
       1, 1, 1, 0, 1, 1])
In [ ]:
print("correct predictions: ", np.sum(y_pred==HCC1806_hyponormo))
print("fraction of correct predictions", np.sum(y_pred==HCC1806_hyponormo) / len(y_pred))
array_errors = []
argwhere_errors = []
for i, j, k in zip( y_pred, HCC1806_hyponormo, range(len(y_pred))):
    if i!=j:
        array_errors.append(HCC1806_f_n.iloc[:,k])
        argwhere_errors.append(k)
print(argwhere_errors) 
position_all_errors["HCC1806"] = argwhere_errors
correct predictions:  170
fraction of correct predictions 0.9340659340659341
[3, 9, 11, 22, 30, 57, 94, 98, 113, 137, 141, 143]

In this case we can see that GMM performed slightly worse than in the previous case, predicting only 93% of correct results.

Again, we will keep track of the errors and, for the same reasons explained before we will check them in the classifier.

comments on the GMM on dropseq

We tried to apply this unsupervised classification method, based on the gaussian probability distribution also on the set cell lines sequentiated with the technique dropseq.

PREDICTIONS

Aim: We are willing to predict whether a cell is in the ‘hypoxia’ or ‘normoxia’ condition based on the specific expressed genes by a given cell line.

Encoding: In our setting, we will refer to the conditions as ‘0’ for hypoxia and ‘1’ for normoxia.

Introduction

As the overarching theme of our draft for a classifier, we have always stored 10% of the data points away from the training set. In this manner, we will remove any further bias from the analysis during the actual testing procedure.

SmartSeq

Having successfully carried the Exploratory Data Analysis (EDA) part, we have gained relevant insights on the dataset which can be used for the classification part. Under this assumption, an initial idea was to implement a Decision Forest so that we could rank the genes available according to the ‘information gain’ criteria. Indeed, using ‘entropy’ as a criterion for the splitting and pruning in the algorithm we could yield a high cross-validation score.

Nonetheless, our final take was to cross-check our assumptions by running other classifiers and, instead of coming down to a final choice, undertake a hard-voting system which could choose the most suitable one. Among the choices available, we have run a Support Vector Machine – using a radial kernel for a greater granular classification and a 50% maximum margin of error – as well as a Logistic Regression. In the latter, a L1 penalty term regularizer yielded the most accurate results yet, given that each competing model made (few) errors on different cells, we were convinced by hard-voting as the best course of action.

Importing the relevant datasets

In [ ]:
%matplotlib inline
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from sklearn.decomposition import PCA
from scipy.cluster.hierarchy import dendrogram
from sklearn.cluster import KMeans , AgglomerativeClustering 
from sklearn.model_selection import train_test_split
import tensorflow as tf
from tensorflow import keras
from sklearn.ensemble import RandomForestClassifier, VotingClassifier
from sklearn.metrics import accuracy_score
from sklearn.svm import NuSVC
from sklearn.linear_model import LogisticRegression

Reading the files:

In [ ]:
# HCC1806_f_n =pd.read_csv('HCC1806_SmartS_Filtered_Normalised_3000_Data_train.txt',delimiter='\ ',engine='python',index_col=0)
# MCF7_f_n = pd.read_csv('MCF7_SmartS_Filtered_Normalised_3000_Data_train.txt',delimiter='\ ',engine='python',index_col=0)

Marking hypoxia as (0) or normoxia as (1) as usual:

In [ ]:
index = MCF7_f_n.T.index
MCF7_hyponormo = np.zeros((len(index)),dtype = 'int64')
for i in range(len(index)):
    MCF7_hyponormo[i] = not 'Hypo' in index[i] # 0 Hypo 1 Norm
In [ ]:
index = HCC1806_f_n.T.index
HCC1806_hyponormo = np.zeros((len(index)),dtype = 'int64')
for i in range(len(index)):
    HCC1806_hyponormo[i] = not 'Hypo' in index[i] # 0 Hypo 1 Norm

Splitting in test and training set:

In [ ]:
MCF7_training, MCF7_testing, MCF7_training_target , MCF7_testing_target = train_test_split(MCF7_f_n.T, MCF7_hyponormo, test_size= 0.1, random_state= 42)
In [ ]:
HCC1806_training, HCC1806_testing, HCC1806_training_target , HCC1806_testing_target = train_test_split(HCC1806_f_n.T, HCC1806_hyponormo, test_size= 0.1, random_state= 42)

We want to emphasize that, in the full code of our analysis, we will not touch the test set created in this instance. In this manner, we will exclude further bias in our classification algorithms and the test set accuracy will be statistically significant.

SmartSeq Classification

Recognizing the Cells from SmartSeq

First of all, we start by training a random forest classifier so that we are able to select the suitable cell line.

The random forest is run on the merged datasets of MCF7 and HCC1806, both filtered and normalized.

The dependent variable where we will fit our random forest to is an array made of 0s if the row belongs to MCF7, of 1s for HCC1806

In [ ]:
MH_f_n = MCF7_f_n.join(HCC1806_f_n, how="outer")
MH_f_n_no = MH_f_n.fillna(0)
MH_f_n_no.T

MC_HC_target =np.concatenate((np.zeros(250, dtype = 'int64'), np.ones(182,dtype = 'int64'))) #0 MCF7 #1 HCC1806
My_cell = RandomForestClassifier(criterion= 'entropy', random_state= 42)
My_cell.fit(MH_f_n_no.T, MC_HC_target)
Out[ ]:
RandomForestClassifier(criterion='entropy', random_state=42)
In [ ]:
XHM_train, XHM_test, yHM_train, yHM_test = train_test_split(MH_f_n_no.T , MC_HC_target, test_size=0.2, shuffle = True,  random_state=42)

As shown, the predictions on the Random Forest Classifier on the test set yield an accuracy of 1.0, so the classifier is able to distinguish the cells coming from SmartSeq.

In [ ]:
My_cell.fit(XHM_train,yHM_train)
accuracy_score(My_cell.predict(XHM_test), yHM_test)
Out[ ]:
1.0

Random Forest on MCF7

We will now run a random forest on MCF7 with information gain entropy as a criterion for choosing the features in splitting. It yields an accuracy of 99.5% on the test set.

We also use cross-validation.

In [ ]:
from sklearn.model_selection import cross_val_score

my_classM = RandomForestClassifier( criterion= 'entropy', random_state= 42)
scoresD = cross_val_score(my_classM, MCF7_training, MCF7_training_target, cv=10)
print(scoresD.mean())

my_classM.fit(MCF7_training, MCF7_training_target)
accuracy_score(MCF7_testing_target, my_classM.predict(MCF7_testing))
0.9956521739130434
Out[ ]:
1.0

Random Forest on HCC1806

On HCC1806 we have a mean of the scores a bit lower, at 98.7%. We keep using the 10-fold cross-validation to achieve the optimal parameters.

In [ ]:
my_classH = RandomForestClassifier(criterion= 'entropy', random_state= 42)
scoresH = cross_val_score(my_classH,HCC1806_training, HCC1806_training_target, cv=10)
print(scoresH.mean())

my_classH.fit(HCC1806_training, HCC1806_training_target)
accuracy_score(HCC1806_testing_target, my_classH.predict(HCC1806_testing))
0.9878676470588236
Out[ ]:
1.0

Support Vector Machine on HCC1806

Subsequently, we run a Nu-Support Vector Classification as a further classifier. 'nu' is an upper bound on the fraction of margin errors and a lower bound of the fraction of support vectors, which should be in the interval (0, 1].

We also use a non-linear kernel and a 10-fold cross validation. The accuracy is 95.77%, and we furthermore check that it works as planned on the testing set and its target.

In [ ]:
my_svmH = NuSVC(nu = 0.3)
scores = cross_val_score(my_svmH, HCC1806_training, HCC1806_training_target, cv=10)
print(scores.mean())

my_svmH.fit(HCC1806_training,HCC1806_training_target)
accuracy_score(my_svmH.predict(HCC1806_testing), HCC1806_testing_target)
0.9577205882352942
Out[ ]:
1.0

Support Vector Machine on MCF7

With the same argument, we run a SVM classifier on MCF7 and obtain a higher accuracy score, int the same fashion we had for other classifiers when comparing MCF7 with HCC1806.

In [ ]:
my_svmM = NuSVC(nu = 0.3)
scoresM = cross_val_score(my_svmM, MCF7_training, MCF7_training_target, cv=10)
print(scoresM.mean())

my_svmM.fit(MCF7_training, MCF7_training_target)
accuracy_score(my_svmM.predict(MCF7_testing), MCF7_testing_target )
0.9913043478260869
Out[ ]:
1.0

We also run a Logistic Regression on MCF7 and HCC1806 as a further classifier. Most importantly, we use a l1-penalty regularizer with the ‘solver’ set to 'liblinear'.

logistic - mcf7

In [ ]:
my_logM = LogisticRegression(solver = "liblinear", penalty="l1", random_state=42) 
scoresM = cross_val_score(my_logM, MCF7_training, MCF7_training_target, cv=10)
print(scoresM.mean())
my_logM.fit(MCF7_training, MCF7_training_target)
accuracy_score(my_logM.predict(MCF7_testing), MCF7_testing_target )
1.0
Out[ ]:
1.0

logistic - HCC1806

The Logistic Regression is slightly less effective on HCC1806.

In [ ]:
my_logH = LogisticRegression(solver = "liblinear", penalty="l1", random_state=42) 
scoresH = cross_val_score(my_logH, HCC1806_training, HCC1806_training_target, cv=10)
print(scoresH.mean())
my_logH.fit(HCC1806_training, HCC1806_training_target)
accuracy_score(my_logH.predict(HCC1806_testing), HCC1806_testing_target )
0.99375
Out[ ]:
1.0

Hard Voting on MCF7

As a next step, we will compare the various classifiers according to the dataset we have feeded into them and the accuracy score we obtain. We have the option of choosing between a hard, binary vote system or a soft one.

If ‘hard’, the class object uses the predicted class labels for majority rule voting. Else, if ‘soft’, it predicts the class label based on the argmax of the sums of the predicted probabilities.

We also have the option to choose the sequence of weights to weight the occurrences of predicted class labels, but since it is set to None, we use uniform weights.

In [ ]:
votingM = VotingClassifier(estimators=[('lr', my_logM), ('rf', my_classM), ('svc', my_svmM)],
                           voting = "hard", weights= None)

votingM.fit(MCF7_training, MCF7_training_target)
accuracy_score(votingM.predict(MCF7_testing), MCF7_testing_target )
Out[ ]:
1.0

Hard Voting on HCC1806

In [ ]:
votingH = VotingClassifier(estimators=[('lr', my_logH), ('rf', my_classH), ('svc', my_svmH)],
                           voting = "hard", weights= None)

votingH.fit(HCC1806_training, HCC1806_training_target)
accuracy_score(votingH.predict(HCC1806_testing), HCC1806_testing_target )
Out[ ]:
1.0

Classifier Function for SmartSeq

It is now time to gather all the classifier we have done into a single, overarching function.

The function takes as input the test dataset given by the professor, and returns whether each single cell, according to its gene characteristics, belongs to the normoxia or hypoxia class.

We have thus decided to create a stratified classifier, where we will use different classifier according to the cell which is identified in the input, whether it belongs to MCF7 or HCC1806.

Initializing a suitable dataframe for the input:

In [ ]:
# fill row
def fill_row(x):
    x = x.to_frame()
    x1 = x.join(MH_f_n_no, lsuffix="z", how = 'outer')
    x1_no = x1.fillna(0)
    x1_no = x1_no.iloc[:,0]
    cell = pd.DataFrame(x1_no.values.reshape(-1, 1), index = x1_no.index.values)
    return  cell.T
In [ ]:
# FOR A SINGLE CELL
def classifier_smartseq(x): 
    
    cell = pd.DataFrame(x.values.reshape(-1, 1), index = x.index.values).T
    x1 = fill_row(x)
    
    if My_cell.predict(x1)[0]:                     # 1 = HCC1806
        """print(" the cell is of line HCC1806")
        if votingH.predict(cell)[0]:               # 1 Norm
            #print(" the cell is in  Normoxia state")
        else: 
            #print(" the cell is in Hypoxia state")"""
        
        return  ["HCC1806", votingH.predict(cell)[0],"Norm" if votingH.predict(cell)[0] else "Hypo" ]

    else:                                          # 0 = MCF7
        """   #print(" the cell is of line MCF7")
        
        if votingM.predict(cell)[0]:               # 1 = Norm
           
             #print(" the cell is in  Normoxia state")
        else: 
            
            #print(" the cell is in Hypoxia state")"""
        return  ["MCF7", votingM.predict(cell)[0],"Norm" if votingM.predict(cell)[0] else "Hypo" ]

Creating a dictionary with the results:

In [ ]:
### classifier for data frame 
def classifier_smartseq_dataframe(df):
   
    results = {}

    for column in df:

        results[str(column)] = classifier_smartseq(df[column])
    
    results = pd.DataFrame.from_dict(results)
    results = results.rename(index={0:'class',1: "state", 2: "state_name"})
    return results

Does our function work?

In [ ]:
trial = pd.read_csv("XCells_SmartS_Filtered_Normalised_3000_Data_test_anonim.txt",delimiter='\ ',engine='python',index_col=0)
In [ ]:
q = classifier_smartseq_dataframe(trial)
In [ ]:
q
Out[ ]:
"1" "2" "3" "4" "5" "6" "7" "8" "9" "10" ... "99" "100" "101" "102" "103" "104" "105" "106" "107" "108"
class MCF7 MCF7 MCF7 MCF7 MCF7 MCF7 MCF7 MCF7 MCF7 MCF7 ... MCF7 MCF7 MCF7 MCF7 MCF7 MCF7 MCF7 MCF7 MCF7 MCF7
state 0 0 1 1 1 1 1 0 0 1 ... 0 0 0 1 1 1 1 0 1 1
state_name Hypo Hypo Norm Norm Norm Norm Norm Hypo Hypo Norm ... Hypo Hypo Hypo Norm Norm Norm Norm Hypo Norm Norm

3 rows × 108 columns

Classifying the anonymous cells

In [ ]:
anonimsM = pd.read_csv("/Users/mariamorandini/Downloads/MCF7_SmartS_Filtered_Normalised_3000_Data_test_anonim (1).txt",delimiter='\ ',engine='python',index_col=0)
anonimsH = pd.read_csv("HCC1806_SmartS_Filtered_Normalised_3000_Data_test_anonim.txt",delimiter='\ ',engine='python',index_col=0)
In [ ]:
H = classifier_smartseq_dataframe(anonimsH)
In [ ]:
M = classifier_smartseq_dataframe(anonimsM)
In [ ]:
M
In [ ]:
H
Out[ ]:
"1" "2" "3" "4" "5" "6" "7" "8" "9" "10" ... "36" "37" "38" "39" "40" "41" "42" "43" "44" "45"
class HCC1806 HCC1806 HCC1806 HCC1806 HCC1806 HCC1806 HCC1806 HCC1806 HCC1806 HCC1806 ... HCC1806 HCC1806 HCC1806 HCC1806 HCC1806 HCC1806 HCC1806 HCC1806 HCC1806 HCC1806
state 1 1 0 0 0 0 0 1 1 1 ... 0 1 1 1 0 0 1 0 1 1
state_name Norm Norm Hypo Hypo Hypo Hypo Hypo Norm Norm Norm ... Hypo Norm Norm Norm Hypo Hypo Norm Hypo Norm Norm

3 rows × 45 columns

Exporting to Excel format

In [ ]:
H.to_excel("output_hcc1806_smartseq.xlsx")
In [ ]:
M.to_excel("output_mcf7_smartseq.xlsx")

Results

After submitting the predictions for the SmartSeq dataset, we got the following results:

For MCF7:\ Out of 63 total cases, we predicted correctly 100% of them.\ 32/32 normoxic cells were correclty classified.\ 31/31 hypoxic cells were correctly classified.

For HCC1806:\ Out of 45 cells, we predicted correctly 95.556 of them.\ 24/26 normoxic cells were correctly classified.\ 19/19 hypoxic cells were correctly classified.\ 2 cells were classified wrongly as hypoxic when they were actually normoxic.

DropSeq

In the DropSeq dataset, a first idea to run the same classifiers was eventually dropped out due to the computational power required to sift through a much higher dimensional dataset. Albeit we left these algorithms free to run for the reader (it will take time!) – without being able to cross validate our results - eventually we opted for a Multi-Layer Perceptron.

Our Neural Network, therefore, will consist of 5 layers which use the ‘SoftMax’ approach. SoftMax converts a vector of values to a probability distribution. The elements of the output vector are in range (0, 1) and sum to 1, where each vector is handled independently. The axis argument in Keras sets which axis of the input the function is applied along.

Overall, this classifier yields a better performance compared the other algorithms we had used thus far.

In [ ]:
%matplotlib inline
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from sklearn.decomposition import PCA
from scipy.cluster.hierarchy import dendrogram
from sklearn.cluster import KMeans , AgglomerativeClustering 
from sklearn.model_selection import train_test_split
import tensorflow as tf
from tensorflow import keras
from sklearn.ensemble import RandomForestClassifier, VotingClassifier
from sklearn.metrics import accuracy_score
from sklearn.svm import NuSVC
from sklearn.linear_model import LogisticRegression
from sklearn.model_selection import cross_val_score
In [ ]:
# MCF7_f_n_drop = pd.read_csv('MCF7_Filtered_Normalised_3000_Data_train.txt', delimiter = '\ ', index_col=0,engine='python')

# Added the following line to use the upload from before
MCF7_f_n_drop = MCF7_drop_f_n
MCF7_f_n_drop.columns = [str(i)+"_m" for i in MCF7_f_n_drop.columns]
In [ ]:
# HCC1806_f_n_drop = pd.read_csv('HCC1806_Filtered_Normalised_3000_Data_train.txt', delimiter = '\ ', engine = 'python', index_col= 0)

# Added the following line to use the upload before
HCC1806_f_n_drop = HCC1806_drop_f_n
In [ ]:
index = HCC1806_f_n_drop.T.index
HCC1806_hyponormo_drop = np.zeros((len(index)),dtype = 'int64')
for i in range(len(index)):
    HCC1806_hyponormo_drop[i] = not 'Hypo' in index[i] # 0 Hypo 1 Norm
In [ ]:
index = MCF7_f_n_drop.T.index
MCF7_hyponormo_drop = np.zeros((len(index)),dtype = 'int64')
for i in range(len(index)):
    MCF7_hyponormo_drop[i] = not 'Hypo' in index[i] # 0 Hypo 1 Norm
In [ ]:
MCF7_drop_training, MCF7_drop_testing, MCF7_drop_training_target , MCF7_drop_testing_target = train_test_split(MCF7_f_n_drop.T, MCF7_hyponormo_drop, test_size= 0.1, random_state= 42)
In [ ]:
HCC1806_drop_training, HCC1806_drop_testing, HCC1806_drop_training_target , HCC1806_drop_testing_target = train_test_split(HCC1806_f_n_drop.T, HCC1806_hyponormo_drop, test_size= 0.1, random_state= 42)

selecting cell line in dropseq

In [ ]:
## here we train a random forest to being able to select the cell line 

MH_f_n_drop = MCF7_f_n_drop.join(HCC1806_f_n_drop, how="outer")
MH_f_n_no_drop = MH_f_n_drop.fillna(0)
MH_f_n_no_drop.T
MC_HC_target_drop =np.concatenate((np.zeros(len(MCF7_hyponormo_drop), dtype = 'int64'), np.ones(len(HCC1806_hyponormo_drop),dtype = 'int64'))) #0 MCF7 #1 HCC1806
In [ ]:
XHMd_train, XHMd_test, yHMd_train, yHMd_test = train_test_split(MH_f_n_no_drop.T , MC_HC_target_drop, test_size=0.2, shuffle = True,  random_state=42)
My_cell_d = RandomForestClassifier(criterion= 'entropy', random_state= 42)
scoresD = cross_val_score(My_cell_d, XHMd_train, yHMd_train, cv=10)
print(scoresD.mean())
My_cell_d.fit(MH_f_n_no_drop.T, MC_HC_target_drop)
accuracy_score(My_cell_d.predict(XHMd_test),yHMd_test)
1.0
Out[ ]:
1.0

extra: canonical classifiers on dropseq

Remark: In the following section are reported the cells to run the canonical classifiers on dropseq, we still decided to share them as this was our first approach. We then decided to use a clever and faster way to classifiy these larger data sets, that is trought the use of neural networks. We thus warn that the run of these cells might take a huge amount of time, so feel free to skip them.

random forest - MCF7

In [ ]:
my_classM = RandomForestClassifier( criterion= 'entropy', random_state= 21 )
scoresD = cross_val_score(my_classM, MCF7_drop_training, MCF7_drop_training_target, cv=10)
print(scoresD.mean())
my_classM.fit(MCF7_drop_training, MCF7_drop_training_target)
accuracy_score(MCF7_drop_testing_target, my_classM.predict(MCF7_drop_testing))
0.9672200518255878
Out[ ]:
0.9667128987517337

random forest - HCC1806

In [ ]:
my_classHd = RandomForestClassifier( criterion= 'entropy', random_state= 21 )
scoresD = cross_val_score(my_classHd, HCC1806_drop_training, HCC1806_drop_training_target, cv=10)
print(scoresD.mean())
my_classHd.fit(HCC1806_drop_training, HCC1806_drop_training_target)
accuracy_score(HCC1806_drop_testing_target, my_classHd.predict(HCC1806_drop_testing))
0.9342315052663765
Out[ ]:
0.9353301565690946

svm - MCF7

In [ ]:
my_svmMd = NuSVC(nu = 0.3)
# scoresM = cross_val_score(my_svmMd, MCF7_drop_training, MCF7_drop_training_target, cv=10)
# print(scoresM.mean())
my_svmMd.fit(MCF7_drop_training, MCF7_drop_training_target)
accuracy_score(my_svmMd.predict(MCF7_drop_testing), MCF7_drop_testing_target )
Out[ ]:
0.9602404068423486

svm - HCC1806

In [ ]:
my_svmHd = NuSVC(nu = 0.3)
# scores = cross_val_score(my_svmH, HCC1806_drop_training, HCC1806_drop_training_target, cv=10)
# print(scores.mean())
my_svmHd.fit(HCC1806_drop_training,HCC1806_drop_training_target)
#my_svmH.decision_function
accuracy_score(my_svmHd.predict(HCC1806_drop_testing), HCC1806_drop_testing_target )
Out[ ]:
0.9489448604492853

logistic regression - MCF7

In [ ]:
my_logMd = LogisticRegression(solver = "liblinear", penalty="l1", random_state=42) 
my_logMd.fit(MCF7_drop_training, MCF7_drop_training_target)
accuracy_score(my_logMd.predict(MCF7_drop_testing), MCF7_drop_testing_target )
Out[ ]:
0.9736477115117892

logistic regression - HCC1806

In [ ]:
my_logHd = LogisticRegression(solver = "liblinear", penalty="l1", random_state=42) 
my_logHd.fit(HCC1806_drop_training, HCC1806_drop_training_target)
accuracy_score(my_logHd.predict(HCC1806_drop_testing), HCC1806_drop_testing_target )
Out[ ]:
0.953710006807352

neural network for HCC1806_drop

In this setting, we use the sparse categorical cross entropy method which expresses the format in which we mention true labels. If they are integers, you usually use sparse_categorical_crossentropy.

One advantage of using sparse categorical cross entropy is it saves time in memory as well as computation because it simply uses a single integer for a class, rather than a whole vector.

Moreover, we use the 'accuracy' metrics to calculate how often predictions equal labels. This metric creates two local variables, total and count that are used to compute the frequency with which y_pred matches y_true. This frequency is ultimately returned as binary accuracy: an idempotent operation that simply divides total by count.

In [ ]:
XH_train, XH_test, yH_train, yH_test = train_test_split(HCC1806_drop_training,HCC1806_drop_training_target, test_size=0.2, random_state=42)
In [ ]:
modelH = keras.models.Sequential()
modelH.add(keras.layers.Flatten(input_shape=[3000]))
modelH.add(keras.layers.Dense(190, activation="relu"))
modelH.add(keras.layers.Dense(120, activation="relu"))
modelH.add(keras.layers.Dense(20, activation="relu"))
modelH.add(keras.layers.Dense(2, activation = 'softmax'))
modelH.compile(loss="sparse_categorical_crossentropy",
              optimizer="sgd",
              metrics=["accuracy"])

Here, we use the ModelCheckpoint callback which is used in conjunction with training using model.fit() to save a model or weights (in a checkpoint file) at some interval, so the model or weights can be loaded later to continue the training from the state saved.

Also, we use EarlyStopping to stop training when a monitored metric has stopped improving.

In [ ]:
mc = keras.callbacks.ModelCheckpoint('best_model_H.h5', monitor='val_accuracy', mode='max', save_best_only=True)
es=keras.callbacks.EarlyStopping(monitor='val_accuracy',mode='max', patience=12)
In [ ]:
modelHC = modelH.fit(XH_train, yH_train, epochs= 30,callbacks = [es,mc],
                  validation_data= (XH_test, yH_test))
Epoch 1/30
331/331 [==============================] - 4s 9ms/step - loss: 0.3230 - accuracy: 0.8623 - val_loss: 0.2045 - val_accuracy: 0.9111
Epoch 2/30
331/331 [==============================] - 3s 8ms/step - loss: 0.1563 - accuracy: 0.9406 - val_loss: 0.1544 - val_accuracy: 0.9414
Epoch 3/30
331/331 [==============================] - 3s 8ms/step - loss: 0.1214 - accuracy: 0.9531 - val_loss: 0.1480 - val_accuracy: 0.9421
Epoch 4/30
331/331 [==============================] - 3s 8ms/step - loss: 0.0993 - accuracy: 0.9630 - val_loss: 0.1365 - val_accuracy: 0.9474
Epoch 5/30
331/331 [==============================] - 3s 8ms/step - loss: 0.0857 - accuracy: 0.9680 - val_loss: 0.1207 - val_accuracy: 0.9531
Epoch 6/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0696 - accuracy: 0.9743 - val_loss: 0.1223 - val_accuracy: 0.9523
Epoch 7/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0593 - accuracy: 0.9801 - val_loss: 0.1197 - val_accuracy: 0.9557
Epoch 8/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0502 - accuracy: 0.9837 - val_loss: 0.1731 - val_accuracy: 0.9330
Epoch 9/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0420 - accuracy: 0.9872 - val_loss: 0.2139 - val_accuracy: 0.9304
Epoch 10/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0349 - accuracy: 0.9910 - val_loss: 0.1260 - val_accuracy: 0.9561
Epoch 11/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0288 - accuracy: 0.9932 - val_loss: 0.1185 - val_accuracy: 0.9591
Epoch 12/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0229 - accuracy: 0.9944 - val_loss: 0.1276 - val_accuracy: 0.9580
Epoch 13/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0188 - accuracy: 0.9966 - val_loss: 0.1264 - val_accuracy: 0.9569
Epoch 14/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0144 - accuracy: 0.9979 - val_loss: 0.1281 - val_accuracy: 0.9591
Epoch 15/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0113 - accuracy: 0.9990 - val_loss: 0.1339 - val_accuracy: 0.9588
Epoch 16/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0094 - accuracy: 0.9992 - val_loss: 0.1340 - val_accuracy: 0.9576
Epoch 17/30
331/331 [==============================] - 3s 9ms/step - loss: 0.0074 - accuracy: 0.9995 - val_loss: 0.1347 - val_accuracy: 0.9599
Epoch 18/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0055 - accuracy: 0.9997 - val_loss: 0.1406 - val_accuracy: 0.9603
Epoch 19/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0044 - accuracy: 0.9998 - val_loss: 0.1412 - val_accuracy: 0.9614
Epoch 20/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0037 - accuracy: 0.9999 - val_loss: 0.1517 - val_accuracy: 0.9572
Epoch 21/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0031 - accuracy: 1.0000 - val_loss: 0.1481 - val_accuracy: 0.9591
Epoch 22/30
331/331 [==============================] - 3s 8ms/step - loss: 0.0028 - accuracy: 1.0000 - val_loss: 0.1479 - val_accuracy: 0.9610
Epoch 23/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0024 - accuracy: 1.0000 - val_loss: 0.1491 - val_accuracy: 0.9610
Epoch 24/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0021 - accuracy: 1.0000 - val_loss: 0.1535 - val_accuracy: 0.9603
Epoch 25/30
331/331 [==============================] - 3s 10ms/step - loss: 0.0019 - accuracy: 1.0000 - val_loss: 0.1523 - val_accuracy: 0.9618
Epoch 26/30
331/331 [==============================] - 3s 8ms/step - loss: 0.0017 - accuracy: 1.0000 - val_loss: 0.1560 - val_accuracy: 0.9595
Epoch 27/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0016 - accuracy: 1.0000 - val_loss: 0.1580 - val_accuracy: 0.9595
Epoch 28/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0014 - accuracy: 1.0000 - val_loss: 0.1578 - val_accuracy: 0.9610
Epoch 29/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0013 - accuracy: 1.0000 - val_loss: 0.1601 - val_accuracy: 0.9610
Epoch 30/30
331/331 [==============================] - 2s 7ms/step - loss: 0.0012 - accuracy: 1.0000 - val_loss: 0.1610 - val_accuracy: 0.9607
In [ ]:
from keras.models import load_model
HCC_nn_bestmodel = load_model('best_model_H.h5')
In [ ]:
c = HCC_nn_bestmodel.predict(HCC1806_drop_testing)
accuracy_score(c.argmax(1), HCC1806_drop_testing_target)
Out[ ]:
0.9591558883594282

neural network for MCF7_drop

In [ ]:
XM_train, XM_test, yM_train, yM_test = train_test_split(MCF7_drop_training,MCF7_drop_training_target, test_size=0.2, random_state=42)
In [ ]:
model = keras.models.Sequential()
model.add(keras.layers.Flatten(input_shape=[3000]))
model.add(keras.layers.Dense(150, activation="relu"))
model.add(keras.layers.Dense(100, activation="relu"))
model.add(keras.layers.Dense(40, activation="relu"))
model.add(keras.layers.Dense(2, activation = 'softmax'))
model.compile(loss="sparse_categorical_crossentropy",
              optimizer="sgd",
              metrics=["accuracy"])
In [ ]:
mc = keras.callbacks.ModelCheckpoint('best_model.h5', monitor='val_accuracy', mode='max', save_best_only=True)
es=keras.callbacks.EarlyStopping(monitor='val_accuracy',mode='max', patience=12)
In [ ]:
modelM = model.fit(XM_train, yM_train, epochs=30, callbacks= [es, mc]  , 
                   validation_data= (XM_test, yM_test))
Epoch 1/30
487/487 [==============================] - 4s 7ms/step - loss: 0.1858 - accuracy: 0.9347 - val_loss: 0.0786 - val_accuracy: 0.9733
Epoch 2/30
487/487 [==============================] - 3s 7ms/step - loss: 0.0714 - accuracy: 0.9746 - val_loss: 0.0607 - val_accuracy: 0.9792
Epoch 3/30
487/487 [==============================] - 3s 7ms/step - loss: 0.0572 - accuracy: 0.9805 - val_loss: 0.0590 - val_accuracy: 0.9825
Epoch 4/30
487/487 [==============================] - 4s 8ms/step - loss: 0.0520 - accuracy: 0.9827 - val_loss: 0.0524 - val_accuracy: 0.9825
Epoch 5/30
487/487 [==============================] - 4s 7ms/step - loss: 0.0412 - accuracy: 0.9863 - val_loss: 0.0994 - val_accuracy: 0.9735
Epoch 6/30
487/487 [==============================] - 4s 8ms/step - loss: 0.0369 - accuracy: 0.9879 - val_loss: 0.0642 - val_accuracy: 0.9782
Epoch 7/30
487/487 [==============================] - 4s 7ms/step - loss: 0.0331 - accuracy: 0.9898 - val_loss: 0.0512 - val_accuracy: 0.9800
Epoch 8/30
487/487 [==============================] - 3s 7ms/step - loss: 0.0286 - accuracy: 0.9915 - val_loss: 0.0577 - val_accuracy: 0.9802
Epoch 9/30
487/487 [==============================] - 4s 7ms/step - loss: 0.0261 - accuracy: 0.9931 - val_loss: 0.0527 - val_accuracy: 0.9807
Epoch 10/30
487/487 [==============================] - 3s 7ms/step - loss: 0.0229 - accuracy: 0.9933 - val_loss: 0.0541 - val_accuracy: 0.9818
Epoch 11/30
487/487 [==============================] - 4s 8ms/step - loss: 0.0204 - accuracy: 0.9945 - val_loss: 0.0523 - val_accuracy: 0.9851
Epoch 12/30
487/487 [==============================] - 3s 6ms/step - loss: 0.0196 - accuracy: 0.9952 - val_loss: 0.0538 - val_accuracy: 0.9820
Epoch 13/30
487/487 [==============================] - 3s 7ms/step - loss: 0.0168 - accuracy: 0.9960 - val_loss: 0.0506 - val_accuracy: 0.9825
Epoch 14/30
487/487 [==============================] - 3s 7ms/step - loss: 0.0145 - accuracy: 0.9972 - val_loss: 0.0507 - val_accuracy: 0.9846
Epoch 15/30
487/487 [==============================] - 3s 7ms/step - loss: 0.0136 - accuracy: 0.9972 - val_loss: 0.0536 - val_accuracy: 0.9820
Epoch 16/30
487/487 [==============================] - 3s 7ms/step - loss: 0.0114 - accuracy: 0.9979 - val_loss: 0.0548 - val_accuracy: 0.9815
Epoch 17/30
487/487 [==============================] - 3s 7ms/step - loss: 0.0109 - accuracy: 0.9978 - val_loss: 0.0556 - val_accuracy: 0.9815
Epoch 18/30
487/487 [==============================] - 3s 7ms/step - loss: 0.0087 - accuracy: 0.9986 - val_loss: 0.0556 - val_accuracy: 0.9818
Epoch 19/30
487/487 [==============================] - 3s 7ms/step - loss: 0.0096 - accuracy: 0.9984 - val_loss: 0.0600 - val_accuracy: 0.9825
Epoch 20/30
487/487 [==============================] - 3s 7ms/step - loss: 0.0075 - accuracy: 0.9987 - val_loss: 0.0671 - val_accuracy: 0.9771
Epoch 21/30
487/487 [==============================] - 4s 7ms/step - loss: 0.0085 - accuracy: 0.9986 - val_loss: 0.0612 - val_accuracy: 0.9805
Epoch 22/30
487/487 [==============================] - 4s 7ms/step - loss: 0.0072 - accuracy: 0.9988 - val_loss: 0.0557 - val_accuracy: 0.9833
Epoch 23/30
487/487 [==============================] - 4s 7ms/step - loss: 0.0074 - accuracy: 0.9987 - val_loss: 0.0574 - val_accuracy: 0.9836
In [ ]:
MCF7_nn_best = load_model('best_model.h5')
In [ ]:
g = MCF7_nn_best.predict(MCF7_drop_testing)
accuracy_score(g.argmax(1), MCF7_drop_testing_target)
Out[ ]:
0.9787332408691632

Results

After submitting the predictions for the DropSeq dataset, we got the following results:

For MCF7:\ Out of 5406 cells, we predicted correctly 98.02% of them.\ 3163/3215 normoxic cells were correctly classified.\ 2136/2191 hypoxic cells were correctly classified.\ 52 cells were classified wrongly as hypoxic when they were actually normoxic.\ 55 cells were classified wrongly as normoxic when they were actually hypoxic.

For HCC1806:\ Out of 3671 cells, we predicted correctly 95.45 of them.\ 1388/1454 normoxic cells were correctly classified.\ 2116/2217 hypoxic cells were correctly classified.\ 66 cells were classified wrongly as hypoxic when they were actually normoxic.\ 101 cells were classified wrongly as normoxic when they were actually hypoxic.

General classifier

Given the task at hand, we build a final classifier so that it can sort our cells based on the ‘cell_type’ parameter, since we do not know a priori the cell line we should receive in the test set. For this reason, we have decided to employ a Random Forest to get a peek on the most expressed genes (as aforementioned). We then sort according to which genes are most expressed in a given cell line and which are the least expressed.

Finally, we coded an overarching function which can take a completely general input from all the dataset and returns the adequate classifier by recognize its origin.

In [ ]:
# fill row
def fill_row_d(x):
    x = x.to_frame()
    x1 = x.join(MH_f_n_no_drop, lsuffix="z", how = 'outer')
    x1_no = x1.fillna(0)
    x1_no = x1_no.iloc[:,0]
    cell = pd.DataFrame(x1_no.values.reshape(-1, 1), index = x1_no.index.values)
    return  cell.T
In [ ]:
# FOR A SINGLE CELL
def classifier_dropseq_cell(x):    
    cell = pd.DataFrame(x.values.reshape(-1, 1), index = x.index.values).T
    x1 = fill_row_d(x)
    if My_cell_d.predict(x1)[0]:                     # 1 = HCC1806
        # NN for HCC1806+
        return  ["HCC1806", (HCC_nn_bestmodel.predict(cell)).argmax(1)[0],"Norm" if (HCC_nn_bestmodel.predict(cell)).argmax(1)[0] else "Hypo" ]
    else:                                          # 0 = MCF7
       # NN for MCF7
        return  ["MCF7", (MCF7_nn_best.predict(cell)).argmax(1)[0],"Norm" if (MCF7_nn_best.predict(cell)).argmax(1)[0] else "Hypo" ]
In [ ]:
# NN result for mcf7
def classifier_mcf7_d(x):
    pred = MCF7_nn_best.predict(x.T).argmax(1)
    res  = []
    for  i   in  pred:
        res.append(["MCF7",  i, "norm" if i else "hypo"])
    res = pd.DataFrame(res).T
    res = res.rename(index ={0:'class',1: "state", 2: "state_name"})
    return res
In [ ]:
# NN result for HCC1806
def classifier_hcc1806_d(x):
    pred = HCC_nn_bestmodel.predict(x.T).argmax(1)
    res  = []
    for  i   in  pred:
        res.append(["HCC1806",  i, "norm" if i else "hypo"])
    res = pd.DataFrame(res).T
    res = res.rename(index ={0:'class',1: "state", 2: "state_name"})
    return res
In [ ]:
# general classsifier for dropseq:
# - this one runs faster but assumes that the data set is only of one kind i.e. takes one sample
# - to decide the whole classifier

def classifier_dropseq(x):
    sample = x.iloc[:, 0]
    sample = fill_row_d(sample)
    
    if My_cell_d.predict(sample)[0]:  # 1 = HCC1806
        return classifier_hcc1806_d(x)
    else:                             # 0 = MCF7
        return classifier_mcf7_d(x)
In [ ]:
# more general classifier- checks cell by cell - Run very slowly, to use only in the case of mixed 
def classifier_dropseq_general(x):
    results = {}
    for column in x:
        results[str(column)] = classifier_dropseq_cell(x[column])
        
    results = pd.DataFrame.from_dict(results)
    results = results.rename(index={0:'class',1: "state", 2: "state_name"})
    return results

classifing the given data set

In [ ]:
anonyms_Md =  pd.read_csv("MCF7_Filtered_Normalised_3000_Data_test_anonim.txt", delimiter = '\ ', index_col=0,engine='python')
anonyms_Hd =  pd.read_csv("HCC1806_Filtered_Normalised_3000_Data_test_anonim.txt", delimiter = '\ ', index_col=0,engine='python' )
In [ ]:
Md = classifier_dropseq(anonyms_Md)
Hd = classifier_dropseq(anonyms_Hd)
In [ ]:
Md
In [ ]:
Hd
In [ ]:
## save outputs 
Hd.to_excel("output_hcc1806_dropseq.xlsx")
Md.to_excel("output_mcf7_dropseq.xlsx")